knitr::opts_chunk$set(echo = TRUE)
rm(list = ls())
#cmdstanr::set_cmdstan_path(path = "C:/Users/kueng/.cmdstan/cmdstan-2.35.0")
#cmdstanr::set_cmdstan_path(path = "C:/Users/pascku/.cmdstan/cmdstan-2.36.0")
library(tidyverse)
library(R.utils)
library(wbCorr)
library(readxl)
library(kableExtra)
library(brms)
library(bayesplot)
library(see)
library(beepr)
library(DHARMa)
library(digest)
library(tidybayes)
library(ggplot2)
source(file.path('Functions', 'ReportModels.R'))
source(file.path('Functions', 'PrettyTables.R'))
source(file.path('Functions', 'ReportMeasures.R'))
source(file.path('Functions', 'PrepareData.R'))
report_function_hash <- digest::digest(summarize_brms)## [1] 1116
# Set options for analysis
use_mi = FALSE
shutdown = FALSE
report_ordinal = FALSE
do_priorsense = FALSE
get_bayesfactor = TRUE
check_models = TRUE
if (get_bayesfactor) {
stats_to_report <- c('CI', 'SE', 'pd', 'ROPE', 'BF', 'Rhat', 'ESS')
} else {
stats_to_report <- c('CI', 'SE', 'pd', 'ROPE', 'Rhat', 'ESS')
}
options(
dplyr.print_max = 100,
brms.backend = 'cmdstan',
brms.file_refit = ifelse(use_mi, 'never', 'on_change'),
brms.file_refit = 'on_change',
#brms.file_refit = 'always',
error = function() {
beepr::beep(sound = 5)
if (shutdown) {
system("shutdown /s /t 180")
quit(save = "no", status = 1)
}
}
, es.use_symbols = TRUE
)
####################### Model parameters #######################
iterations = 12000 # 12'000 per chain to achieve 40'000
warmup = 2000 # 2000
# NO AR!!!
#corstr = 'ar'
#corstr = 'cosy_couple'
#corstr = 'cosy_couple:user'
################################################################
suffix = paste0('_SensitivityBarriersFacilitatorsInteract_', as.character(iterations))df <- openxlsx::read.xlsx(file.path('long.xlsx'))
df_original <- df
df_double <- prepare_data(df, recode_pushing = TRUE, use_mi = use_mi)[[1]]Constructing scales Re-coding pusing reshaping data (4field) centering data within and between
Min. 1st Qu. Median Mean 3rd Qu. Max. NA’s 0.0000 0.0000 0.0000 0.1649 0.0000 5.0000 275
# For indistinguishable Dyads
model_rows_fixed <- c(
'Intercept',
# '-- WITHIN PERSON MAIN EFFECTS --',
'persuasion_self_cw',
'persuasion_partner_cw',
'pressure_self_cw',
'pressure_partner_cw',
'pushing_self_cw',
'pushing_partner_cw',
'day',
'plan_selfPlan',
'plan_partnerPlan', # todo: do we need this??
'barriers_self_cw',
'barriers_partner_cw',
'facilitators_self_cw',
'facilitators_partner_cw',
'weartime_self_cw',
# '-- BETWEEN PERSON MAIN EFFECTS',
'persuasion_self_cb',
'persuasion_partner_cb',
'pressure_self_cb',
'pressure_partner_cb',
'pushing_self_cb',
'pushing_partner_cb',
'barriers_self_cb',
'barriers_partner_cb',
'facilitators_self_cb',
'facilitators_partner_cb',
'weartime_self_cb',
# Interactions
'persuasion_self_cw:barriers_self_cw',
'barriers_self_cw:persuasion_self_cw',
'pressure_self_cw:barriers_self_cw',
'barriers_self_cw:pressure_self_cw',
'pushing_self_cw:barriers_self_cw',
'barriers_self_cw:pushing_self_cw',
'persuasion_self_cw:facilitators_self_cw',
'facilitators_self_cw:persuasion_self_cw',
'pressure_self_cw:facilitators_self_cw',
'facilitators_self_cw:pressure_self_cw',
'pushing_self_cw:facilitators_self_cw',
'facilitators_self_cw:pushing_self_cw',
'persuasion_partner_cw:barriers_self_cw',
'barriers_self_cw:persuasion_partner_cw',
'pressure_partner_cw:barriers_self_cw',
'barriers_self_cw:pressure_partner_cw',
'pushing_partner_cw:barriers_self_cw',
'barriers_self_cw:pushing_partner_cw',
'persuasion_partner_cw:facilitators_self_cw',
'facilitators_self_cw:persuasion_partner_cw',
'pressure_partner_cw:facilitators_self_cw',
'facilitators_self_cw:pressure_partner_cw',
'pushing_partner_cw:facilitators_self_cw',
'facilitators_self_cw:pushing_partner_cw',
'persuasion_self_cw:barriers_partner_cw',
'barriers_partner_cw:persuasion_self_cw',
'pressure_self_cw:barriers_partner_cw',
'barriers_partner_cw:pressure_self_cw',
'pushing_self_cw:barriers_partner_cw',
'barriers_partner_cw:pushing_self_cw',
'persuasion_self_cw:facilitators_partner_cw',
'facilitators_partner_cw:persuasion_self_cw',
'pressure_self_cw:facilitators_partner_cw',
'facilitators_partner_cw:pressure_self_cw',
'pushing_self_cw:facilitators_partner_cw',
'facilitators_partner_cw:pushing_self_cw',
'persuasion_partner_cw:barriers_partner_cw',
'barriers_partner_cw:persuasion_partner_cw',
'pressure_partner_cw:barriers_partner_cw',
'barriers_partner_cw:pressure_partner_cw',
'pushing_partner_cw:barriers_partner_cw',
'barriers_partner_cw:pushing_partner_cw',
'persuasion_partner_cw:facilitators_partner_cw',
'facilitators_partner_cw:persuasion_partner_cw',
'pressure_partner_cw:facilitators_partner_cw',
'facilitators_partner_cw:pressure_partner_cw',
'pushing_partner_cw:facilitators_partner_cw',
'facilitators_partner_cw:pushing_partner_cw'
)
model_rows_fixed_ordinal <- c(
model_rows_fixed[1],
'Intercept[1]',
'Intercept[2]',
'Intercept[3]',
'Intercept[4]',
'Intercept[5]',
model_rows_fixed[2:length(model_rows_fixed)]
)
model_rows_random <- c(
# '--------------',
# '-- RANDOM EFFECTS --',
'sd(Intercept)',
'sd(persuasion_self_cw)',
'sd(persuasion_partner_cw)',
'sd(pressure_self_cw)',
'sd(pressure_partner_cw)',
'sd(pushing_self_cw)',
'sd(pushing_partner_cw)',
'sd(barriers_self_cw)',
'sd(barriers_partner_cw)',
'sd(facilitators_self_cw)',
'sd(facilitators_partner_cw)',
# '-- CORRELATION STRUCTURE -- ',
'sigma'
)
model_rows_random_ordinal <- c(model_rows_random,'disc')# For indistinguishable Dyads
model_rownames_fixed <- c(
"Intercept",
# "-- WITHIN PERSON MAIN EFFECTS --",
"Daily individual's experienced persuasion",
"Daily partner's experienced persuasion",
"Daily individual's experienced pressure",
"Daily partner's experienced pressure",
"Daily individual's experienced pushing",
"Daily partner's experienced pushing",
"Day",
"Own action plan",
'Partner action plan',
"Daily individuals' barriers",
"Daily partners' barriers",
"Daily individuals' facilitators",
"Daily partners' facilitators",
"Daily wear time",
# "-- BETWEEN PERSON MAIN EFFECTS",
"Mean individual's experienced persuasion",
"Mean partner's experienced persuasion",
"Mean individual's experienced pressure",
"Mean partner's experienced pressure",
"Mean individual's experienced pushing",
"Mean partner's experienced pushing",
"Mean individuals' barriers",
"Mean partners' barriers",
"Mean individuals' facilitators",
"Mean partners' facilitators",
"Mean wear time",
# Interactions
'persuasion_self_cw:barriers_self_cw',
'barriers_self_cw:persuasion_self_cw',
'pressure_self_cw:barriers_self_cw',
'barriers_self_cw:pressure_self_cw',
'pushing_self_cw:barriers_self_cw',
'barriers_self_cw:pushing_self_cw',
'persuasion_self_cw:facilitators_self_cw',
'facilitators_self_cw:persuasion_self_cw',
'pressure_self_cw:facilitators_self_cw',
'facilitators_self_cw:pressure_self_cw',
'pushing_self_cw:facilitators_self_cw',
'facilitators_self_cw:pushing_self_cw',
'persuasion_partner_cw:barriers_self_cw',
'barriers_self_cw:persuasion_partner_cw',
'pressure_partner_cw:barriers_self_cw',
'barriers_self_cw:pressure_partner_cw',
'pushing_partner_cw:barriers_self_cw',
'barriers_self_cw:pushing_partner_cw',
'persuasion_partner_cw:facilitators_self_cw',
'facilitators_self_cw:persuasion_partner_cw',
'pressure_partner_cw:facilitators_self_cw',
'facilitators_self_cw:pressure_partner_cw',
'pushing_partner_cw:facilitators_self_cw',
'facilitators_self_cw:pushing_partner_cw',
'persuasion_self_cw:barriers_partner_cw',
'barriers_partner_cw:persuasion_self_cw',
'pressure_self_cw:barriers_partner_cw',
'barriers_partner_cw:pressure_self_cw',
'pushing_self_cw:barriers_partner_cw',
'barriers_partner_cw:pushing_self_cw',
'persuasion_self_cw:facilitators_partner_cw',
'facilitators_partner_cw:persuasion_self_cw',
'pressure_self_cw:facilitators_partner_cw',
'facilitators_partner_cw:pressure_self_cw',
'pushing_self_cw:facilitators_partner_cw',
'facilitators_partner_cw:pushing_self_cw',
'persuasion_partner_cw:barriers_partner_cw',
'barriers_partner_cw:persuasion_partner_cw',
'pressure_partner_cw:barriers_partner_cw',
'barriers_partner_cw:pressure_partner_cw',
'pushing_partner_cw:barriers_partner_cw',
'barriers_partner_cw:pushing_partner_cw',
'persuasion_partner_cw:facilitators_partner_cw',
'facilitators_partner_cw:persuasion_partner_cw',
'pressure_partner_cw:facilitators_partner_cw',
'facilitators_partner_cw:pressure_partner_cw',
'pushing_partner_cw:facilitators_partner_cw',
'facilitators_partner_cw:pushing_partner_cw'
)
model_rownames_fixed_ordinal <- c(
model_rownames_fixed[1],
'Intercept[1]',
'Intercept[2]',
'Intercept[3]',
'Intercept[4]',
'Intercept[5]',
model_rownames_fixed[2:length(model_rownames_fixed)]
)
model_rownames_random <- c(
# '--------------',
# '-- RANDOM EFFECTS --',
'sd(Intercept)',
"sd(Daily individual's experienced persuasion)",
"sd(Daily partner's experienced persuasion)", # OR partner received
"sd(Daily individual's experienced pressure)",
"sd(Daily partner's experienced pressure)",
"sd(Daily individual's experienced pushing)",
"sd(Daily partner's experienced pushing)",
'sd(barriers_self_cw)',
'sd(barriers_partner_cw)',
'sd(barriers_partner_cw)',
'sd(facilitators_self_cw)',
'sd(facilitators_partner_cw)',
# '-- CORRELATION STRUCTURE -- ',
'sigma'
)
model_rownames_random_ordinal <- c(model_rownames_random,'disc')rows_to_pack <- list(
"Within-Person Effects" = c(2,15),
"Between-Person Effects" = c(16,26),
"Interactions" = c(27, 74),
"Random Effects" = c(75, 85),
"Additional Parameters" = c(86,86)
)
rows_to_pack_ordinal <- list(
"Within-Person Effects" = c(2+5,15+5),
"Between-Person Effects" = c(16+5,26+5),
"Interactions" = c(27+5, 74+5),
"Random Effects" = c(75+5, 85+5),
"Additional Parameters" = c(86+5,86+6)
)Speficy interactions
interaction_terms <- paste(
'+ persuasion_self_cw * barriers_self_cw',
'+ pressure_self_cw * barriers_self_cw',
'+ pushing_self_cw * barriers_self_cw',
#'+ persuasion_self_cw * facilitators_self_cw',
#'+ pressure_self_cw * facilitators_self_cw',
#'+ pushing_self_cw * facilitators_self_cw',
'+ persuasion_partner_cw * barriers_self_cw',
'+ pressure_partner_cw * barriers_self_cw',
'+ pushing_partner_cw * barriers_self_cw',
#'+ persuasion_partner_cw * facilitators_self_cw',
#'+ pressure_partner_cw * facilitators_self_cw',
#'+ pushing_partner_cw * facilitators_self_cw',
#'+ persuasion_self_cw * barriers_partner_cw',
#'+ pressure_self_cw * barriers_partner_cw',
#'+ pushing_self_cw * barriers_partner_cw',
#'+ persuasion_self_cw * facilitators_partner_cw',
#'+ pressure_self_cw * facilitators_partner_cw',
#'+ pushing_self_cw * facilitators_partner_cw',
#'+ persuasion_partner_cw * barriers_partner_cw',
#'+ pressure_partner_cw * barriers_partner_cw',
#'+ pushing_partner_cw * barriers_partner_cw',
#'+ persuasion_partner_cw * facilitators_partner_cw',
#'+ pressure_partner_cw * facilitators_partner_cw',
#'+ pushing_partner_cw * facilitators_partner_cw',
""
)
formula_terms <- paste(
"~ 1",
"+ persuasion_self_cw + persuasion_partner_cw",
"+ pressure_self_cw + pressure_partner_cw",
"+ pushing_self_cw + pushing_partner_cw",
"+ persuasion_self_cb + persuasion_partner_cb",
"+ pressure_self_cb + pressure_partner_cb",
"+ pushing_self_cb + pushing_partner_cb",
"+ barriers_self_cb + facilitators_self_cb",
#"+ barriers_partner_cb + facilitators_partner_cb",
"+ day",
#"+ weartime_self_cw + weartime_self_cb",
interaction_terms,
"+ (1",
"+ persuasion_self_cw + persuasion_partner_cw",
"+ pressure_self_cw + pressure_partner_cw",
"+ pushing_self_cw + pushing_partner_cw",
interaction_terms,
"| dd | coupleID)"
)## [1] 0 720
formula <- bf(
as.formula(
paste("pa_sub", formula_terms)
),
hu = as.formula(
formula_terms
)
, decomp = 'QR'
#, autocor = autocor_str
)
prior1 <- c(
brms::set_prior("normal(0, 2.5)", class = "b")
, brms::set_prior("normal(0, 2)", class = "b", dpar = "hu")
, brms::set_prior("normal(0, 50)", class = "Intercept") # for non-zero PA
, brms::set_prior("normal(0.5, 2.5)", class = "Intercept", dpar = 'hu') # hurdle part
, brms::set_prior("normal(0, 2)", class = "sd", group = "coupleID", lb = 0)
, brms::set_prior("student_t(3, 0, 2.5)", class = "sigma", lb = 0)
)
#brms::validate_prior(
# prior1,
# formula = formula,
# data = df_double,
# family = hurdle_lognormal()
#)
#df_minimal <- df_double[, c("AorB", all.vars(as.formula(formula)))]
pa_sub <- my_brm(
mi = use_mi,
imputed_data = implist,
formula = formula,
prior = prior1,
data = df_double,
family = brms::hurdle_lognormal(),
#family = brms::hurdle_negbinomial(),
#family = brms::hurdle_poisson(),
#control = list(adapt_delta = 0.90),
iter = iterations,
warmup = warmup,
chains = 4,
cores = 4,
seed = 42,
file = file.path("models_cache_brms", paste0("pa_sub_hu_lognormal", suffix))
#, file_refit = 'always'
)## Warning: Rows containing NAs were excluded from the model.
## Start sampling
if (check_models) {
check_brms(pa_sub, log_pp_check = TRUE)
DHARMa.check_brms.all(pa_sub, integer = TRUE, outliers_type = 'bootstrap')
}## # Check for Multicollinearity
##
## Low Correlation
##
## Term VIF VIF 95% CI Increased SE Tolerance
## persuasion_self_cw 1.31 [1.30, 1.32] 1.14 0.76
## persuasion_partner_cw 1.09 [1.08, 1.10] 1.04 0.92
## pressure_self_cw 1.08 [1.08, 1.09] 1.04 0.92
## pressure_partner_cw 1.06 [1.05, 1.07] 1.03 0.94
## pushing_self_cw 1.06 [1.05, 1.07] 1.03 0.94
## pushing_partner_cw 1.10 [1.09, 1.11] 1.05 0.91
## persuasion_self_cb 1.06 [1.05, 1.07] 1.03 0.94
## persuasion_partner_cb 3.91 [3.86, 3.95] 1.98 0.26
## pressure_self_cb 3.83 [3.79, 3.88] 1.96 0.26
## pressure_partner_cb 2.30 [2.28, 2.33] 1.52 0.43
## pushing_self_cb 2.24 [2.22, 2.27] 1.50 0.45
## pushing_partner_cb 3.13 [3.09, 3.17] 1.77 0.32
## barriers_self_cb 3.14 [3.10, 3.17] 1.77 0.32
## facilitators_self_cb 1.10 [1.09, 1.11] 1.05 0.91
## day 1.09 [1.08, 1.10] 1.04 0.92
## barriers_self_cw 1.27 [1.26, 1.28] 1.13 0.79
## Tolerance 95% CI
## [0.76, 0.77]
## [0.91, 0.92]
## [0.92, 0.93]
## [0.93, 0.95]
## [0.94, 0.95]
## [0.90, 0.91]
## [0.94, 0.95]
## [0.25, 0.26]
## [0.26, 0.26]
## [0.43, 0.44]
## [0.44, 0.45]
## [0.32, 0.32]
## [0.32, 0.32]
## [0.90, 0.91]
## [0.91, 0.93]
## [0.78, 0.80]
## # Distribution of Model Family
##
## Predicted Distribution of Residuals
##
## Distribution Probability
## cauchy 91%
## lognormal 9%
##
## Predicted Distribution of Response
##
## Distribution Probability
## neg. binomial (zero-infl.) 84%
## beta-binomial 9%
## lognormal 6%
##
## Divergences:
## 0 of 40000 iterations ended with a divergence.
##
## Tree depth:
## 0 of 40000 iterations saturated the maximum tree depth of 10.
##
## Energy:
## E-BFMI indicated no pathological behavior.
## Using 10 posterior draws for ppc type 'ecdf_overlay' by default.
## Using 10 posterior draws for ppc type 'dens_overlay' by default.
## Warning: Found 31 observations with a pareto_k > 0.7 in model 'model'.
## We recommend to set 'moment_match = TRUE' in order to perform moment
## matching for problematic observations.
##
## DHARMa bootstrapped outlier test
##
## data: model.check
## outliers at both margin(s) = 5, observations = 1776, p-value =
## 0.4
## alternative hypothesis: two.sided
## percent confidence interval:
## 0.00000000 0.00423705
## sample estimates:
## outlier frequency (expected: 0.00170045045045045 )
## 0.002815315
if (do_priorsense) {
priorsense_vars <- c(
'Intercept',
'b_persuasion_self_cw',
'b_persuasion_partner_cw',
'b_pressure_self_cw',
'b_pressure_partner_cw',
'b_pushing_self_cw',
'b_pushing_partner_cw'
)
hurdle_priorsense_vars <- c(
'Intercept_hu',
'b_hu_persuasion_self_cw',
'b_hu_persuasion_partner_cw',
'b_hu_pressure_self_cw',
'b_hu_pressure_partner_cw',
'b_hu_pushing_self_cw',
'b_hu_pushing_partner_cw'
)
gc()
priorsense::powerscale_sensitivity(pa_sub, variable = c(priorsense_vars, hurdle_priorsense_vars))
priorsense::powerscale_plot_dens(pa_sub, variable = c(priorsense_vars, hurdle_priorsense_vars))
priorsense::powerscale_plot_ecdf(pa_sub, variable = c(priorsense_vars, hurdle_priorsense_vars))
priorsense::powerscale_plot_quantities(pa_sub, variable = c(priorsense_vars, hurdle_priorsense_vars))
}# rope range for continuous part of the model
rope_factor <- sd(log(pa_sub$data$pa_sub[pa_sub$data$pa_sub > 0]))
rope_range_continuous = c(-0.1 * rope_factor, 0.1 * rope_factor)
summary_pa_sub <- summarize_brms(
pa_sub,
stats_to_report = stats_to_report,
rope_range = rope_range_continuous,
hu_rope_range = c(-0.18, 0.18),
model_rows_fixed = model_rows_fixed,
model_rows_random = model_rows_random,
model_rownames_fixed = model_rownames_fixed,
model_rownames_random = model_rownames_random,
exponentiate = T) ## Sampling priors, please wait...
## Warning in summarize_brms(pa_sub, stats_to_report = stats_to_report,
## rope_range = rope_range_continuous, : Coefficients were exponentiated.
## Double check if this was intended.
## Warning in summarize_brms(pa_sub, stats_to_report = stats_to_report,
## rope_range = rope_range_continuous, : Some rows from the model were
## omitted due to your provided model_rows_fixed or model_rows_random
## vectors. Missing rows: sd(persuasion_partner_cw:barriers_self_cw),
## sd(persuasion_self_cw:barriers_self_cw),
## sd(pressure_partner_cw:barriers_self_cw),
## sd(pressure_self_cw:barriers_self_cw),
## sd(pushing_partner_cw:barriers_self_cw),
## sd(pushing_self_cw:barriers_self_cw)
## Warning in summarize_brms(pa_sub, stats_to_report = stats_to_report,
## rope_range = rope_range_continuous, : Length of model_rownames does not
## match number of rows
| exp(Est.)_hu | SE_hu | 95% CI_hu | pd_hu | ROPE_hu | inside ROPE_hu | BF_hu | BF_Evidence_hu | Rhat_hu | Bulk_ESS_hu | Tail_ESS_hu | exp(Est.)_nonzero | SE_nonzero | 95% CI_nonzero | pd_nonzero | ROPE_nonzero | inside ROPE_nonzero | BF_nonzero | BF_Evidence_nonzero | Rhat_nonzero | Bulk_ESS_nonzero | Tail_ESS_nonzero | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Intercept | 2.89*** | 0.83 | [ 1.62, 5.14] | 1.000 | [0.84, 1.20] | 0.002 | 46.729 | Very Strong Evidence | 1.000 | 36107 | 32627 | 49.15*** | 4.02 | [41.78, 58.06] | 1.000 | [0.93, 1.08] | 0.000 | >100 | Overwhelming Evidence | 1.000 | 14059 | 20647 |
| Within-Person Effects | ||||||||||||||||||||||
| persuasion_self_cw | 1.61*** | 0.19 | [ 1.30, 2.07] | 1.000 | [0.84, 1.20] | 0.003 | >100 | Overwhelming Evidence | 1.000 | 47652 | 31218 | 1.04 | 0.03 | [ 0.99, 1.10] | 0.928 | [0.93, 1.08] | 0.904 | 0.029 | Very Strong Evidence for Null | 1.000 | 32436 | 32732 |
| persuasion_partner_cw | 1.44*** | 0.16 | [ 1.17, 1.86] | 1.000 | [0.84, 1.20] | 0.041 | 18.216 | Strong Evidence | 1.000 | 44125 | 31400 | 1.02 | 0.02 | [ 0.98, 1.07] | 0.811 | [0.93, 1.08] | 0.988 | 0.013 | Very Strong Evidence for Null | 1.000 | 45651 | 33711 |
| pressure_self_cw | 0.84 | 0.28 | [ 0.43, 1.92] | 0.698 | [0.84, 1.20] | 0.356 | 0.198 | Moderate Evidence for Null | 1.000 | 36472 | 24492 | 0.90 | 0.06 | [ 0.78, 1.03] | 0.946 | [0.93, 1.08] | 0.305 | 0.041 | Strong Evidence for Null | 1.000 | 40255 | 31489 |
| pressure_partner_cw | 1.64 | 0.65 | [ 0.85, 5.26] | 0.923 | [0.84, 1.20] | 0.171 | 0.443 | Weak Evidence for Null | 1.000 | 27246 | 24271 | 0.96 | 0.05 | [ 0.86, 1.06] | 0.791 | [0.93, 1.08] | 0.756 | 0.012 | Very Strong Evidence for Null | 1.000 | 44440 | 34295 |
| pushing_self_cw | 1.22 | 0.23 | [ 0.82, 1.84] | 0.854 | [0.84, 1.20] | 0.428 | 0.176 | Moderate Evidence for Null | 1.000 | 39647 | 30278 | 0.98 | 0.03 | [ 0.92, 1.05] | 0.701 | [0.93, 1.08] | 0.950 | 0.011 | Very Strong Evidence for Null | 1.000 | 39607 | 37174 |
| pushing_partner_cw | 1.60* | 0.36 | [ 1.07, 2.78] | 0.989 | [0.84, 1.20] | 0.077 | 1.609 | Weak Evidence | 1.000 | 34873 | 26963 | 0.96 | 0.03 | [ 0.90, 1.02] | 0.907 | [0.93, 1.08] | 0.854 | 0.021 | Very Strong Evidence for Null | 1.000 | 41168 | 36861 |
| day | 0.88 | 0.22 | [ 0.54, 1.42] | 0.702 | [0.84, 1.20] | 0.480 | 0.140 | Moderate Evidence for Null | 1.000 | 83049 | 31083 | 1.03 | 0.07 | [ 0.89, 1.18] | 0.647 | [0.93, 1.08] | 0.684 | 0.009 | Very Strong Evidence for Null | 1.000 | 73504 | 30624 |
| plan_selfPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| plan_partnerPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_self_cw | 0.68 | 0.17 | [ 0.42, 1.12] | 0.938 | [0.84, 1.20] | 0.185 | 0.432 | Weak Evidence for Null | 1.000 | 37413 | 32446 | 1.08 | 0.06 | [ 0.97, 1.20] | 0.930 | [0.93, 1.08] | 0.493 | 0.040 | Strong Evidence for Null | 1.000 | 36312 | 30151 |
| barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Between-Person Effects | ||||||||||||||||||||||
| persuasion_self_cb | 0.91 | 0.57 | [ 0.25, 3.09] | 0.563 | [0.84, 1.20] | 0.226 | 0.319 | Weak Evidence for Null | 1.000 | 25393 | 28776 | 1.07 | 0.18 | [ 0.76, 1.50] | 0.651 | [0.93, 1.08] | 0.329 | 0.017 | Very Strong Evidence for Null | 1.000 | 23466 | 28917 |
| persuasion_partner_cb | 1.35 | 0.84 | [ 0.38, 4.59] | 0.684 | [0.84, 1.20] | 0.202 | 0.356 | Weak Evidence for Null | 1.000 | 25207 | 28535 | 0.94 | 0.16 | [ 0.67, 1.31] | 0.640 | [0.93, 1.08] | 0.335 | 0.017 | Very Strong Evidence for Null | 1.000 | 21992 | 29105 |
| pressure_self_cb | 0.23 | 0.20 | [ 0.04, 1.24] | 0.956 | [0.84, 1.20] | 0.040 | 1.874 | Weak Evidence | 1.000 | 36118 | 33182 | 0.69 | 0.28 | [ 0.31, 1.59] | 0.816 | [0.93, 1.08] | 0.100 | 0.037 | Strong Evidence for Null | 1.000 | 10355 | 16869 |
| pressure_partner_cb | 0.20 | 0.17 | [ 0.03, 1.03] | 0.972 | [0.84, 1.20] | 0.028 | 2.636 | Weak Evidence | 1.000 | 36552 | 33738 | 0.51 | 0.21 | [ 0.23, 1.17] | 0.946 | [0.93, 1.08] | 0.039 | 0.095 | Strong Evidence for Null | 1.000 | 10275 | 17210 |
| pushing_self_cb | 1.35 | 1.21 | [ 0.23, 7.96] | 0.632 | [0.84, 1.20] | 0.152 | 0.483 | Weak Evidence for Null | 1.000 | 33489 | 31707 | 1.50 | 0.45 | [ 0.83, 2.70] | 0.913 | [0.93, 1.08] | 0.079 | 0.043 | Strong Evidence for Null | 1.000 | 14333 | 21871 |
| pushing_partner_cb | 1.76 | 1.59 | [ 0.30, 10.33] | 0.732 | [0.84, 1.20] | 0.132 | 0.555 | Weak Evidence for Null | 1.000 | 34246 | 32112 | 1.65 | 0.50 | [ 0.91, 2.95] | 0.950 | [0.93, 1.08] | 0.052 | 0.067 | Strong Evidence for Null | 1.000 | 13692 | 23296 |
| barriers_self_cb | 0.50** | 0.13 | [ 0.30, 0.83] | 0.997 | [0.84, 1.20] | 0.023 | 5.072 | Moderate Evidence | 1.000 | 86915 | 31419 | 0.92 | 0.08 | [ 0.78, 1.09] | 0.827 | [0.93, 1.08] | 0.452 | 0.016 | Very Strong Evidence for Null | 1.000 | 56891 | 32994 |
| barriers_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cb | 1.20 | 0.23 | [ 0.82, 1.77] | 0.831 | [0.84, 1.20] | 0.458 | 0.153 | Moderate Evidence for Null | 1.000 | 69399 | 31737 | 1.14* | 0.06 | [ 1.03, 1.27] | 0.992 | [0.93, 1.08] | 0.151 | 0.258 | Moderate Evidence for Null | 1.000 | 38644 | 32619 |
| facilitators_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Interactions | ||||||||||||||||||||||
| persuasion_self_cw:barriers_self_cw | 0.95 | 0.20 | [ 0.62, 1.46] | 0.599 | [0.84, 1.20] | 0.598 | 0.104 | Moderate Evidence for Null | 1.000 | 40097 | 30713 | 0.99 | 0.04 | [ 0.92, 1.07] | 0.570 | [0.93, 1.08] | 0.946 | 0.010 | Very Strong Evidence for Null | 1.000 | 46953 | 33280 |
| barriers_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_self_cw | 0.49 | 0.26 | [ 0.15, 1.54] | 0.906 | [0.84, 1.20] | 0.102 | 0.721 | Weak Evidence for Null | 1.000 | 40753 | 29719 | 1.02 | 0.12 | [ 0.79, 1.31] | 0.557 | [0.93, 1.08] | 0.469 | 0.012 | Very Strong Evidence for Null | 1.000 | 39661 | 31246 |
| barriers_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_self_cw | 1.94 | 0.66 | [ 0.99, 4.10] | 0.973 | [0.84, 1.20] | 0.067 | 1.187 | Weak Evidence | 1.000 | 36948 | 31340 | 0.96 | 0.05 | [ 0.86, 1.07] | 0.777 | [0.93, 1.08] | 0.716 | 0.014 | Very Strong Evidence for Null | 1.000 | 39441 | 33259 |
| barriers_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_self_cw | 0.68* | 0.12 | [ 0.46, 0.95] | 0.989 | [0.84, 1.20] | 0.110 | 1.212 | Weak Evidence | 1.000 | 42700 | 32366 | 1.06 | 0.04 | [ 0.99, 1.13] | 0.946 | [0.93, 1.08] | 0.709 | 0.033 | Strong Evidence for Null | 1.000 | 57612 | 34728 |
| barriers_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_self_cw | 0.82 | 0.44 | [ 0.26, 2.53] | 0.647 | [0.84, 1.20] | 0.245 | 0.281 | Moderate Evidence for Null | 1.000 | 43577 | 31306 | 0.90 | 0.07 | [ 0.75, 1.05] | 0.916 | [0.93, 1.08] | 0.323 | 0.025 | Very Strong Evidence for Null | 1.000 | 42764 | 30340 |
| barriers_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_self_cw | 1.71 | 0.51 | [ 0.99, 3.43] | 0.974 | [0.84, 1.20] | 0.097 | 0.920 | Weak Evidence for Null | 1.000 | 35042 | 30469 | 1.05 | 0.05 | [ 0.95, 1.18] | 0.851 | [0.93, 1.08] | 0.669 | 0.016 | Very Strong Evidence for Null | 1.000 | 45960 | 32440 |
| barriers_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Random Effects | ||||||||||||||||||||||
| sd(Intercept) | 1.44 | 0.22 | [1.08, 1.97] | NA | NA | NA | NA | NA | 1.000 | 27830 | 30182 | 0.31 | 0.05 | [0.23, 0.42] | NA | NA | NA | NA | NA | 1.000 | 18714 | 26238 |
| sd(persuasion_self_cw) | 0.17 | 0.14 | [0.01, 0.51] | NA | NA | NA | NA | NA | 1.000 | 19021 | 21922 | 0.10 | 0.03 | [0.05, 0.16] | NA | NA | NA | NA | NA | 1.000 | 15886 | 16147 |
| sd(persuasion_partner_cw) | 0.20 | 0.15 | [0.01, 0.54] | NA | NA | NA | NA | NA | 1.000 | 16993 | 21418 | 0.05 | 0.03 | [0.01, 0.11] | NA | NA | NA | NA | NA | 1.000 | 14162 | 13842 |
| sd(pressure_self_cw) | 0.54 | 0.48 | [0.03, 2.05] | NA | NA | NA | NA | NA | 1.000 | 17469 | 24791 | 0.08 | 0.07 | [0.00, 0.30] | NA | NA | NA | NA | NA | 1.000 | 19070 | 23257 |
| sd(pressure_partner_cw) | 0.53 | 0.48 | [0.03, 2.08] | NA | NA | NA | NA | NA | 1.000 | 18042 | 23934 | 0.05 | 0.05 | [0.00, 0.20] | NA | NA | NA | NA | NA | 1.000 | 24798 | 22570 |
| sd(pushing_self_cw) | 0.61 | 0.30 | [0.07, 1.30] | NA | NA | NA | NA | NA | 1.000 | 12779 | 12795 | 0.07 | 0.04 | [0.00, 0.16] | NA | NA | NA | NA | NA | 1.000 | 15015 | 19267 |
| sd(pushing_partner_cw) | 0.64 | 0.34 | [0.07, 1.47] | NA | NA | NA | NA | NA | 1.000 | 13111 | 14791 | 0.06 | 0.04 | [0.00, 0.15] | NA | NA | NA | NA | NA | 1.000 | 16130 | 16326 |
| sd(barriers_self_cw) | 1.27 | 0.22 | [0.91, 1.79] | NA | NA | NA | NA | NA | 1.000 | 35412 | 33128 | 0.20 | 0.06 | [0.08, 0.33] | NA | NA | NA | NA | NA | 1.000 | 13833 | 12632 |
| sd(barriers_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_self_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Additional Parameters | ||||||||||||||||||||||
| sigma | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 0.66 | 0.01 | [0.63, 0.69] | NA | NA | NA | NA | NA | 1.000 | 45048 | 31583 |
# Plot continuous part of model
variable <- c(
'(Intercept)',
'b_persuasion_self_cw',
'b_persuasion_partner_cw',
'b_pressure_self_cw',
'b_pressure_partner_cw',
'b_pushing_self_cw',
'b_pushing_partner_cw'
)
plot(
bayestestR::p_direction(pa_sub, parameter = variable),
priors = TRUE
) + theme_bw()## Warning in `==.default`(dens$Parameter, parameter): longer object length
## is not a multiple of shorter object length
## Warning in is.na(e1) | is.na(e2): longer object length is not a multiple
## of shorter object length
plot(
bayestestR::rope(
pa_sub,
parameter = variable,
range = rope_range_continuous,
verbose = F,
ci = 1
)
) + theme_bw()# Hurdle part of the model
variable <- c(
'b_hu_persuasion_self_cw',
'b_hu_persuasion_partner_cw',
'b_hu_pressure_self_cw',
'b_hu_pressure_partner_cw',
'b_hu_pushing_self_cw',
'b_hu_pushing_partner_cw'
)
plot(
bayestestR::p_direction(pa_sub, parameter = variable),
priors = TRUE
) + theme_bw()## Warning in `==.default`(dens$Parameter, parameter): longer object length
## is not a multiple of shorter object length
## Warning in `==.default`(dens$Parameter, parameter): longer object length
## is not a multiple of shorter object length
# The rope range for the bernoulli part of the model is -0.18, 0.18
plot(
bayestestR::rope(pa_sub, parameter = variable, range = c(-0.18, 0.18), ci = 1),
verbose = FALSE
) + theme_bw()## Possible multicollinearity between b_hu_persuasion_partner_cb and
## b_hu_persuasion_self_cb (r = 0.78), b_persuasion_partner_cb and
## b_persuasion_self_cb (r = 0.73), b_pressure_partner_cb and
## b_pressure_self_cb (r = 0.81). This might lead to inappropriate
## results. See 'Details' in '?rope'.
Hurdle part of the model on the left, non-zero part towards the right side of the table
conds_eff <- conditional_spaghetti(
pa_sub,
effects = c(
'persuasion_self_cw',
'persuasion_partner_cw',
'pressure_self_cw',
'pressure_partner_cw',
'pushing_self_cw',
'pushing_partner_cw'
),
x_label = c(
'Received Persuasion',
'Exerted Persuasion',
'Received Pressure',
'Exerted Pressure',
'Received Plan-Related Pushing',
'Exerted Plan-Related Pushing'
),
group_var = 'coupleID',
plot_full_range = TRUE,
y_limits = c(0, 100),
y_label = "Same-Day MVPA",
y_labels = c('Probability of Being Active', 'Minutes of MVPA When Active', 'Overall Expected Minutes of MVPA'),
, filter_quantiles = .9995
, font_family = 'Candara'
)## Scanning ttf files in C:\Windows/Fonts, C:\Users\pascku\AppData\Local/Microsoft/Windows/Fonts ...
## Extracting .afm files from .ttf files...
## C:\Windows\Fonts\Candara.ttf : Candara already registered in fonts database. Skipping.
## C:\Windows\Fonts\Candarab.ttf : Candara-Bold already registered in fonts database. Skipping.
## C:\Windows\Fonts\Candarai.ttf : Candara-Italic already registered in fonts database. Skipping.
## C:\Windows\Fonts\Candaral.ttf : Candara-Light already registered in fonts database. Skipping.
## C:\Windows\Fonts\Candarali.ttf : Candara-LightItalic already registered in fonts database. Skipping.
## C:\Windows\Fonts\Candaraz.ttf : Candara-BoldItalic already registered in fonts database. Skipping.
## Found FontName for 0 fonts.
## Scanning afm files in C:/Users/pascku/AppData/Local/R/cache/R/renv/cache/v5/windows/R-4.4/x86_64-w64-mingw32/extrafontdb/1.0/a861555ddec7451c653b40e713166c6f/extrafontdb/metrics
## Warning: Dropping 'draws_df' class as required metadata was removed.
## Warning: Dropping 'draws_df' class as required metadata was removed.
## Warning: Dropping 'draws_df' class as required metadata was removed.
## Warning: Dropping 'draws_df' class as required metadata was removed.
## Warning: Dropping 'draws_df' class as required metadata was removed.
## Warning: Dropping 'draws_df' class as required metadata was removed.
$persuasion_self_cw
## Warning: Removed 105 rows containing missing values or values outside the scale
## range (`geom_line()`).
## Warning: Removed 211 rows containing missing values or values outside the scale
## range (`geom_line()`).
## Picking joint bandwidth of 0.00958
$persuasion_partner_cw
## Warning: Removed 77 rows containing missing values or values outside the scale
## range (`geom_line()`).
## Warning: Removed 174 rows containing missing values or values outside the scale
## range (`geom_line()`).
## Picking joint bandwidth of 0.00839
$pressure_self_cw
## Warning: Removed 45 rows containing missing values or values outside the scale
## range (`geom_line()`).
## Warning: Removed 89 rows containing missing values or values outside the scale
## range (`geom_line()`).
## Picking joint bandwidth of 0.0159
$pressure_partner_cw
## Warning: Removed 25 rows containing missing values or values outside the scale
## range (`geom_line()`).
## Picking joint bandwidth of 0.0303
$pushing_self_cw
## Warning: Removed 13 rows containing missing values or values outside the scale
## range (`geom_line()`).
## Warning: Removed 35 rows containing missing values or values outside the scale
## range (`geom_line()`).
## Picking joint bandwidth of 0.0116
$pushing_partner_cw
## Warning: Removed 16 rows containing missing values or values outside the scale
## range (`geom_line()`).
## Warning: Removed 43 rows containing missing values or values outside the scale
## range (`geom_line()`).
## Picking joint bandwidth of 0.0166
Note. This graphic illustrates the relationship between
social control and moderate to vigorous physical activity (MVPA) using a
Bayesian Hurdle-Lognormal Multilevel Model. The predictor is centered
within individuals to examine how deviations from their average social
control relate to same-day MVPA. Shaded areas indicate credible
intervals, thick lines show fixed effects, and thin lines represent
random effects, highlighting variability across couples. The plots
display the probability of being active, expected minutes of MVPA when
active, and combined predicted MVPA. The bottom density plot visualizes
the posterior distributions of slope estimates, transformed to represent
multiplicative changes in odds ratios (hurdle component) or expected
values. Medians and 95% credible intervals (2.5th and 97.5th
percentiles) are shown. Effects are significant, when the 95% credible
interval does not overlap 1.
## Hypothesis Tests for class b:
## Hypothesis Estimate Est.Error CI.Lower CI.Upper
## 1 (pressure_self_cw... < 0 -0.09 0.08 -0.23 0.04
## Evid.Ratio Post.Prob Star
## 1 6.62 0.87
## ---
## 'CI': 90%-CI for one-sided and 95%-CI for two-sided hypotheses.
## '*': For one-sided hypotheses, the posterior probability exceeds 95%;
## for two-sided hypotheses, the value tested against lies outside the 95%-CI.
## Posterior probabilities of point hypotheses assume equal prior probabilities.
## [1] 5.75 971.25
formula <- bf(
as.formula(
paste("pa_obj", formula_terms, "+ weartime_self_cw + weartime_self_cb")
)
, decomp = 'QR'
#, autocor = autocor_str
)
prior1 <- c(
brms::set_prior("normal(0, 2.5)", class = "b")
, brms::set_prior("normal(0, 50)", class = "Intercept")
, brms::set_prior("normal(0, 2)", class = "sd", group = "coupleID", lb = 0)
, brms::set_prior("student_t(3, 0, 2.5)", class = "sigma", lb = 0)
)
#brms::validate_prior(
# prior1,
# formula = formula,
# data = df_double,
# family = lognormal()
# )
#df_minimal <- df_double[, c("AorB", all.vars(as.formula(formula)))]
pa_obj_log <- my_brm(
mi = use_mi,
imputed_data = implist,
formula = formula,
prior = prior1,
data = df_double,
family = lognormal(),
control = list(adapt_delta = 0.99),
iter = iterations + 200,
warmup = warmup + 200,
chains = 4,
cores = 4,
seed = 7777,
file = file.path("models_cache_brms", paste0("pa_obj_log_gaussian", suffix))
#, file_refit = 'always'
)## Warning: Rows containing NAs were excluded from the model.
if (check_models) {
check_brms(pa_obj_log, log_pp_check = TRUE)
DHARMa.check_brms.all(pa_obj_log, integer = TRUE, outliers_type = 'bootstrap')
}## # Check for Multicollinearity
##
## Low Correlation
##
## Term VIF VIF 95% CI Increased SE Tolerance
## persuasion_self_cw 1.12 [1.09, 1.16] 1.06 0.89
## persuasion_partner_cw 1.14 [1.11, 1.18] 1.07 0.88
## pressure_self_cw 1.09 [1.06, 1.13] 1.04 0.92
## pressure_partner_cw 1.12 [1.09, 1.16] 1.06 0.89
## pushing_self_cw 1.20 [1.16, 1.24] 1.09 0.83
## pushing_partner_cw 1.20 [1.17, 1.25] 1.10 0.83
## pressure_self_cb 3.66 [3.49, 3.85] 1.91 0.27
## pressure_partner_cb 3.80 [3.62, 4.00] 1.95 0.26
## barriers_self_cb 1.12 [1.09, 1.16] 1.06 0.89
## facilitators_self_cb 1.12 [1.09, 1.16] 1.06 0.89
## day 1.06 [1.04, 1.10] 1.03 0.94
## barriers_self_cw 1.05 [1.02, 1.09] 1.02 0.95
## weartime_self_cw 1.06 [1.04, 1.10] 1.03 0.94
## weartime_self_cb 1.23 [1.19, 1.28] 1.11 0.81
## Tolerance 95% CI
## [0.86, 0.92]
## [0.85, 0.90]
## [0.88, 0.94]
## [0.86, 0.92]
## [0.80, 0.86]
## [0.80, 0.86]
## [0.26, 0.29]
## [0.25, 0.28]
## [0.86, 0.92]
## [0.86, 0.92]
## [0.91, 0.97]
## [0.92, 0.98]
## [0.91, 0.97]
## [0.78, 0.84]
##
## Moderate Correlation
##
## Term VIF VIF 95% CI Increased SE Tolerance
## persuasion_self_cb 6.95 [6.59, 7.33] 2.64 0.14
## persuasion_partner_cb 7.39 [7.01, 7.80] 2.72 0.14
## pushing_self_cb 5.59 [5.30, 5.89] 2.36 0.18
## pushing_partner_cb 5.45 [5.18, 5.74] 2.33 0.18
## Tolerance 95% CI
## [0.14, 0.15]
## [0.13, 0.14]
## [0.17, 0.19]
## [0.17, 0.19]
## # Distribution of Model Family
##
## Predicted Distribution of Residuals
##
## Distribution Probability
## cauchy 88%
## lognormal 9%
## weibull 3%
##
## Predicted Distribution of Response
##
## Distribution Probability
## lognormal 72%
## tweedie 16%
## neg. binomial (zero-infl.) 9%
##
## Divergences:
## 0 of 40000 iterations ended with a divergence.
##
## Tree depth:
## 0 of 40000 iterations saturated the maximum tree depth of 10.
##
## Energy:
## E-BFMI indicated no pathological behavior.
## Using 10 posterior draws for ppc type 'ecdf_overlay' by default.
## Using 10 posterior draws for ppc type 'dens_overlay' by default.
## Warning: Found 2 observations with a pareto_k > 0.7 in model 'model'. We
## recommend to set 'moment_match = TRUE' in order to perform moment
## matching for problematic observations.
## DHARMa:testOutliers with type = binomial may have inflated Type I error rates for integer-valued distributions. To get a more exact result, it is recommended to re-run testOutliers with type = 'bootstrap'. See ?testOutliers for details
##
## DHARMa bootstrapped outlier test
##
## data: model.check
## outliers at both margin(s) = 11, observations = 1594, p-value =
## 0.02
## alternative hypothesis: two.sided
## percent confidence interval:
## 0.000925345 0.006273526
## sample estimates:
## outlier frequency (expected: 0.00310539523212045 )
## 0.006900878
if (do_priorsense) {
gc()
priorsense::powerscale_sensitivity(pa_obj_log, variable = priorsense_vars)
priorsense::powerscale_plot_dens(pa_obj_log, variable = priorsense_vars)
priorsense::powerscale_plot_ecdf(pa_obj_log, variable = priorsense_vars)
priorsense::powerscale_plot_quantities(pa_obj_log, variable = priorsense_vars)
}# rope range for lognormal model
rope_factor <- sd(log(pa_obj_log$data$pa_obj))
rope_range_log = c(-0.1 * rope_factor, 0.1 * rope_factor)
summary_pa_obj <- summarize_brms(
pa_obj_log,
stats_to_report = stats_to_report,
rope_range = rope_range_log,
model_rows_fixed = model_rows_fixed,
model_rows_random = model_rows_random,
model_rownames_fixed = model_rownames_fixed,
model_rownames_random = model_rownames_random,
exponentiate = T) ## Sampling priors, please wait...
## Warning in summarize_brms(pa_obj_log, stats_to_report = stats_to_report,
## : Coefficients were exponentiated. Double check if this was intended.
## Warning in summarize_brms(pa_obj_log, stats_to_report = stats_to_report,
## : Some rows from the model were omitted due to your provided
## model_rows_fixed or model_rows_random vectors. Missing rows:
## sd(persuasion_self_cw:barriers_self_cw),
## sd(pressure_self_cw:barriers_self_cw),
## sd(pushing_self_cw:barriers_self_cw),
## sd(persuasion_partner_cw:barriers_self_cw),
## sd(pressure_partner_cw:barriers_self_cw),
## sd(pushing_partner_cw:barriers_self_cw)
## Warning in summarize_brms(pa_obj_log, stats_to_report = stats_to_report,
## : Length of model_rownames does not match number of rows
| exp(Est.) | SE | 95% CI | pd | ROPE | inside ROPE | BF | BF_Evidence | Rhat | Bulk_ESS | Tail_ESS | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Intercept | 122.92*** | 7.50 | [108.77, 138.83] | 1.000 | [0.94, 1.06] | 0.000 | >100 | Overwhelming Evidence | 1.002 | 6870 | 14120 |
| Within-Person Effects | |||||||||||
| persuasion_self_cw | 1.03 | 0.02 | [ 0.99, 1.06] | 0.908 | [0.94, 1.06] | 0.974 | 0.018 | Very Strong Evidence for Null | 1.000 | 23617 | 27233 |
| persuasion_partner_cw | 1.03 | 0.02 | [ 0.99, 1.07] | 0.950 | [0.94, 1.06] | 0.952 | 0.028 | Very Strong Evidence for Null | 1.000 | 27240 | 26910 |
| pressure_self_cw | 0.95 | 0.05 | [ 0.85, 1.05] | 0.848 | [0.94, 1.06] | 0.563 | 0.013 | Very Strong Evidence for Null | 1.000 | 28839 | 25172 |
| pressure_partner_cw | 0.98 | 0.04 | [ 0.90, 1.06] | 0.726 | [0.94, 1.06] | 0.820 | 0.008 | Very Strong Evidence for Null | 1.000 | 35044 | 28996 |
| pushing_self_cw | 1.03 | 0.03 | [ 0.97, 1.08] | 0.822 | [0.94, 1.06] | 0.902 | 0.012 | Very Strong Evidence for Null | 1.000 | 30297 | 26694 |
| pushing_partner_cw | 0.99 | 0.02 | [ 0.94, 1.04] | 0.655 | [0.94, 1.06] | 0.980 | 0.007 | Very Strong Evidence for Null | 1.000 | 34670 | 27675 |
| day | 0.97 | 0.05 | [ 0.88, 1.07] | 0.725 | [0.94, 1.06] | 0.711 | 0.007 | Very Strong Evidence for Null | 1.000 | 41413 | 31002 |
| plan_selfPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| plan_partnerPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_self_cw | 0.97 | 0.03 | [ 0.91, 1.03] | 0.850 | [0.94, 1.06] | 0.803 | 0.015 | Very Strong Evidence for Null | 1.000 | 24471 | 27118 |
| barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cw | 1.00*** | 0.00 | [ 1.00, 1.00] | 1.000 | [0.94, 1.06] | 1.000 | 1.696 | Weak Evidence | 1.000 | 46240 | 30780 |
| Between-Person Effects | |||||||||||
| persuasion_self_cb | 0.96 | 0.16 | [ 0.69, 1.33] | 0.603 | [0.94, 1.06] | 0.284 | 0.016 | Very Strong Evidence for Null | 1.001 | 5272 | 11415 |
| persuasion_partner_cb | 0.82 | 0.14 | [ 0.59, 1.15] | 0.881 | [0.94, 1.06] | 0.149 | 0.031 | Strong Evidence for Null | 1.001 | 5079 | 10623 |
| pressure_self_cb | 1.16 | 0.21 | [ 0.81, 1.67] | 0.787 | [0.94, 1.06] | 0.195 | 0.013 | Very Strong Evidence for Null | 1.000 | 8234 | 16693 |
| pressure_partner_cb | 1.06 | 0.19 | [ 0.75, 1.51] | 0.638 | [0.94, 1.06] | 0.262 | 0.011 | Very Strong Evidence for Null | 1.000 | 7053 | 14687 |
| pushing_self_cb | 1.14 | 0.27 | [ 0.70, 1.82] | 0.704 | [0.94, 1.06] | 0.177 | 0.015 | Very Strong Evidence for Null | 1.000 | 8007 | 14496 |
| pushing_partner_cb | 1.29 | 0.30 | [ 0.81, 2.06] | 0.863 | [0.94, 1.06] | 0.116 | 0.024 | Very Strong Evidence for Null | 1.000 | 7463 | 14575 |
| barriers_self_cb | 0.78*** | 0.04 | [ 0.70, 0.87] | 1.000 | [0.94, 1.06] | 0.000 | 52.846 | Very Strong Evidence | 1.000 | 40907 | 31422 |
| barriers_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cb | 0.97 | 0.04 | [ 0.89, 1.05] | 0.791 | [0.94, 1.06] | 0.762 | 0.013 | Very Strong Evidence for Null | 1.000 | 25201 | 28784 |
| facilitators_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cb | 1.00* | 0.00 | [ 1.00, 1.00] | 0.989 | [0.94, 1.06] | 1.000 | 0.138 | Moderate Evidence for Null | 1.000 | 23810 | 28177 |
| Interactions | |||||||||||
| persuasion_self_cw:barriers_self_cw | 0.96 | 0.02 | [ 0.92, 1.01] | 0.919 | [0.94, 1.06] | 0.855 | 0.018 | Very Strong Evidence for Null | 1.000 | 34982 | 28834 |
| barriers_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_self_cw | 1.05 | 0.09 | [ 0.89, 1.26] | 0.734 | [0.94, 1.06] | 0.474 | 0.009 | Very Strong Evidence for Null | 1.000 | 24314 | 22052 |
| barriers_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_self_cw | 0.98 | 0.03 | [ 0.91, 1.05] | 0.731 | [0.94, 1.06] | 0.873 | 0.008 | Very Strong Evidence for Null | 1.000 | 33379 | 29877 |
| barriers_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_self_cw | 1.03 | 0.03 | [ 0.98, 1.09] | 0.888 | [0.94, 1.06] | 0.868 | 0.014 | Very Strong Evidence for Null | 1.000 | 33227 | 27717 |
| barriers_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_self_cw | 0.97 | 0.06 | [ 0.85, 1.10] | 0.700 | [0.94, 1.06] | 0.615 | 0.008 | Very Strong Evidence for Null | 1.000 | 34380 | 27698 |
| barriers_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_self_cw | 1.07 | 0.04 | [ 0.99, 1.16] | 0.962 | [0.94, 1.06] | 0.419 | 0.032 | Strong Evidence for Null | 1.000 | 33826 | 28576 |
| barriers_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Random Effects | |||||||||||
| sd(Intercept) | 0.33 | 0.04 | [0.25, 0.43] | NA | NA | NA | NA | NA | 1.000 | 9836 | 18223 |
| sd(persuasion_self_cw) | 0.06 | 0.02 | [0.02, 0.10] | NA | NA | NA | NA | NA | 1.000 | 12418 | 9002 |
| sd(persuasion_partner_cw) | 0.05 | 0.02 | [0.01, 0.10] | NA | NA | NA | NA | NA | 1.001 | 9286 | 8413 |
| sd(pressure_self_cw) | 0.07 | 0.06 | [0.00, 0.24] | NA | NA | NA | NA | NA | 1.000 | 10882 | 15600 |
| sd(pressure_partner_cw) | 0.04 | 0.03 | [0.00, 0.13] | NA | NA | NA | NA | NA | 1.000 | 19515 | 17192 |
| sd(pushing_self_cw) | 0.08 | 0.04 | [0.01, 0.15] | NA | NA | NA | NA | NA | 1.000 | 8938 | 8950 |
| sd(pushing_partner_cw) | 0.05 | 0.03 | [0.00, 0.11] | NA | NA | NA | NA | NA | 1.000 | 11007 | 13575 |
| sd(barriers_self_cw) | 0.14 | 0.03 | [0.08, 0.21] | NA | NA | NA | NA | NA | 1.000 | 17799 | 20265 |
| sd(barriers_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_self_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Additional Parameters | |||||||||||
| sigma | 0.53 | 0.01 | [0.51, 0.55] | NA | NA | NA | NA | NA | 1.000 | 35524 | 29989 |
plot(
bayestestR::p_direction(pa_obj_log),
priors = TRUE
) +
coord_cartesian(xlim = c(-3, 3)) +
theme_bw()## Warning in `==.default`(dens$Parameter, parameter): longer object length
## is not a multiple of shorter object length
## Warning in is.na(e1) | is.na(e2): longer object length is not a multiple
## of shorter object length
## Possible multicollinearity between b_persuasion_partner_cb and
## b_persuasion_self_cb (r = 0.85), b_pressure_partner_cb and
## b_persuasion_partner_cb (r = 0.7), b_pushing_partner_cb and
## b_pushing_self_cb (r = 0.76). This might lead to inappropriate
## results. See 'Details' in '?rope'.
## [1] 0 5
formula <- bf(
as.formula(
paste("aff", formula_terms)
)
, decomp = 'QR'
#, autocor = autocor_str
)
prior1 <- c(
brms::set_prior("normal(0, 5)", class = "b")
,brms::set_prior("normal(0, 20)", class = "Intercept", lb=1, ub=6)
, brms::set_prior("normal(0, 2)", class = "sd", group = "coupleID", lb = 0)
, brms::set_prior("student_t(3, 0, 2.5)", class = "sigma", lb = 0)
)
#brms::validate_prior(
# prior1,
# formula = formula,
# data = df_double,
# family = gaussian()
# )
#df_minimal <- df_double[, c("AorB", all.vars(as.formula(formula)))]
mood_gauss <- my_brm(
mi = use_mi,
imputed_data = implist,
formula = formula,
prior = prior1,
data = df_double,
family = gaussian(),
control = list(adapt_delta = 0.95),
iter = iterations,
warmup = warmup,
chains = 4,
cores = 4,
seed = 7777,
file = file.path("models_cache_brms", paste0("mood_gauss", suffix))
#, file_refit = 'always'
)## Warning: Rows containing NAs were excluded from the model.
if (check_models) {
check_brms(mood_gauss, log_pp_check = FALSE)
DHARMa.check_brms.all(mood_gauss, integer = FALSE)
}## # Check for Multicollinearity
##
## Low Correlation
##
## Term VIF VIF 95% CI Increased SE Tolerance
## persuasion_self_cw 1.17 [1.13, 1.21] 1.08 0.86
## persuasion_partner_cw 1.14 [1.11, 1.18] 1.07 0.88
## pressure_self_cw 1.12 [1.09, 1.16] 1.06 0.89
## pressure_partner_cw 1.07 [1.05, 1.12] 1.04 0.93
## pushing_self_cw 1.26 [1.22, 1.31] 1.12 0.79
## pushing_partner_cw 1.17 [1.13, 1.21] 1.08 0.86
## pressure_self_cb 4.68 [4.44, 4.93] 2.16 0.21
## pressure_partner_cb 4.59 [4.36, 4.84] 2.14 0.22
## barriers_self_cb 1.09 [1.07, 1.14] 1.05 0.91
## facilitators_self_cb 1.08 [1.05, 1.12] 1.04 0.92
## day 1.07 [1.04, 1.11] 1.03 0.94
## barriers_self_cw 1.06 [1.03, 1.10] 1.03 0.95
## Tolerance 95% CI
## [0.82, 0.88]
## [0.84, 0.90]
## [0.86, 0.92]
## [0.90, 0.95]
## [0.76, 0.82]
## [0.83, 0.88]
## [0.20, 0.23]
## [0.21, 0.23]
## [0.88, 0.94]
## [0.89, 0.95]
## [0.90, 0.96]
## [0.91, 0.97]
##
## Moderate Correlation
##
## Term VIF VIF 95% CI Increased SE Tolerance
## persuasion_self_cb 9.89 [9.36, 10.45] 3.14 0.10
## persuasion_partner_cb 9.73 [9.21, 10.29] 3.12 0.10
## pushing_self_cb 7.20 [6.82, 7.61] 2.68 0.14
## pushing_partner_cb 7.27 [6.89, 7.68] 2.70 0.14
## Tolerance 95% CI
## [0.10, 0.11]
## [0.10, 0.11]
## [0.13, 0.15]
## [0.13, 0.15]
## # Distribution of Model Family
##
## Predicted Distribution of Residuals
##
## Distribution Probability
## normal 44%
## cauchy 38%
## exponential 6%
##
## Predicted Distribution of Response
##
## Distribution Probability
## tweedie 41%
## beta-binomial 38%
## half-cauchy 6%
##
## Divergences:
## 0 of 40000 iterations ended with a divergence.
##
## Tree depth:
## 0 of 40000 iterations saturated the maximum tree depth of 10.
##
## Energy:
## E-BFMI indicated no pathological behavior.
## Using 10 posterior draws for ppc type 'ecdf_overlay' by default.
## Using 10 posterior draws for ppc type 'dens_overlay' by default.
## Warning: Found 9 observations with a pareto_k > 0.7 in model 'model'. We
## recommend to set 'moment_match = TRUE' in order to perform moment
## matching for problematic observations.
##
## DHARMa outlier test based on exact binomial test with
## approximate expectations
##
## data: model.check
## outliers at both margin(s) = 7, observations = 1776, p-value =
## 0.09756
## alternative hypothesis: true probability of success is not equal to 0.001998002
## 95 percent confidence interval:
## 0.001586087 0.008103914
## sample estimates:
## frequency of outliers (expected: 0.001998001998002 )
## 0.003941441
if (do_priorsense) {
gc()
priorsense::powerscale_sensitivity(mood_gauss, variable = priorsense_vars)
priorsense::powerscale_plot_dens(mood_gauss, variable = priorsense_vars)
priorsense::powerscale_plot_ecdf(mood_gauss, variable = priorsense_vars)
priorsense::powerscale_plot_quantities(mood_gauss, variable = priorsense_vars)
}summary_mood <- summarize_brms(
mood_gauss,
stats_to_report = stats_to_report,
model_rows_fixed = model_rows_fixed,
model_rows_random = model_rows_random,
model_rownames_fixed = model_rownames_fixed,
model_rownames_random = model_rownames_random,
exponentiate = F) ## Sampling priors, please wait...
## Warning in summarize_brms(mood_gauss, stats_to_report = stats_to_report,
## : Some rows from the model were omitted due to your provided
## model_rows_fixed or model_rows_random vectors. Missing rows:
## sd(persuasion_self_cw:barriers_self_cw),
## sd(pressure_self_cw:barriers_self_cw),
## sd(pushing_self_cw:barriers_self_cw),
## sd(persuasion_partner_cw:barriers_self_cw),
## sd(pressure_partner_cw:barriers_self_cw),
## sd(pushing_partner_cw:barriers_self_cw)
## Warning in summarize_brms(mood_gauss, stats_to_report = stats_to_report,
## : Length of model_rownames does not match number of rows
| Est. | SE | 95% CI | pd | ROPE | inside ROPE | BF | BF_Evidence | Rhat | Bulk_ESS | Tail_ESS | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Intercept | 3.80*** | 0.11 | [ 3.59, 4.02] | 1.000 | [-0.11, 0.11] | 0.000 | >100 | Overwhelming Evidence | 1.000 | 9033 | 16338 |
| Within-Person Effects | |||||||||||
| persuasion_self_cw | 0.01 | 0.02 | [-0.03, 0.06] | 0.694 | [-0.11, 0.11] | 1.000 | 0.005 | Very Strong Evidence for Null | 1.000 | 58478 | 33456 |
| persuasion_partner_cw | 0.01 | 0.02 | [-0.04, 0.06] | 0.649 | [-0.11, 0.11] | 1.000 | 0.005 | Very Strong Evidence for Null | 1.000 | 58878 | 31925 |
| pressure_self_cw | -0.02 | 0.07 | [-0.16, 0.11] | 0.643 | [-0.11, 0.11] | 0.870 | 0.006 | Very Strong Evidence for Null | 1.000 | 51732 | 33773 |
| pressure_partner_cw | -0.04 | 0.06 | [-0.17, 0.08] | 0.749 | [-0.11, 0.11] | 0.862 | 0.006 | Very Strong Evidence for Null | 1.000 | 45660 | 30515 |
| pushing_self_cw | 0.02 | 0.04 | [-0.06, 0.10] | 0.696 | [-0.11, 0.11] | 0.986 | 0.006 | Very Strong Evidence for Null | 1.000 | 43875 | 35961 |
| pushing_partner_cw | 0.08 | 0.04 | [ 0.00, 0.15] | 0.973 | [-0.11, 0.11] | 0.796 | 0.042 | Strong Evidence for Null | 1.000 | 46215 | 32014 |
| day | 0.25** | 0.07 | [ 0.10, 0.39] | 0.999 | [-0.11, 0.11] | 0.036 | 0.804 | Weak Evidence for Null | 1.000 | 77689 | 30117 |
| plan_selfPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| plan_partnerPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_self_cw | -0.26*** | 0.06 | [-0.38, -0.12] | 1.000 | [-0.11, 0.11] | 0.015 | 7.134 | Moderate Evidence | 1.000 | 31242 | 31401 |
| barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Between-Person Effects | |||||||||||
| persuasion_self_cb | 0.07 | 0.29 | [-0.52, 0.63] | 0.591 | [-0.11, 0.11] | 0.292 | 0.014 | Very Strong Evidence for Null | 1.000 | 9257 | 15757 |
| persuasion_partner_cb | 0.33 | 0.28 | [-0.25, 0.89] | 0.872 | [-0.11, 0.11] | 0.159 | 0.027 | Very Strong Evidence for Null | 1.000 | 9132 | 15341 |
| pressure_self_cb | -0.02 | 0.29 | [-0.59, 0.56] | 0.527 | [-0.11, 0.11] | 0.295 | 0.009 | Very Strong Evidence for Null | 1.000 | 11775 | 20704 |
| pressure_partner_cb | -0.27 | 0.29 | [-0.83, 0.31] | 0.825 | [-0.11, 0.11] | 0.192 | 0.014 | Very Strong Evidence for Null | 1.000 | 11380 | 20343 |
| pushing_self_cb | 0.22 | 0.41 | [-0.61, 1.04] | 0.704 | [-0.11, 0.11] | 0.184 | 0.014 | Very Strong Evidence for Null | 1.000 | 11891 | 19705 |
| pushing_partner_cb | 0.01 | 0.41 | [-0.82, 0.82] | 0.507 | [-0.11, 0.11] | 0.213 | 0.012 | Very Strong Evidence for Null | 1.000 | 11933 | 18765 |
| barriers_self_cb | -0.57*** | 0.08 | [-0.72, -0.41] | 1.000 | [-0.11, 0.11] | 0.000 | >100 | Overwhelming Evidence | 1.000 | 78957 | 31536 |
| barriers_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cb | 0.32*** | 0.06 | [ 0.21, 0.44] | 1.000 | [-0.11, 0.11] | 0.000 | >100 | Overwhelming Evidence | 1.000 | 47983 | 32535 |
| facilitators_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Interactions | |||||||||||
| persuasion_self_cw:barriers_self_cw | -0.01 | 0.04 | [-0.09, 0.06] | 0.600 | [-0.11, 0.11] | 0.992 | 0.005 | Very Strong Evidence for Null | 1.000 | 51568 | 32597 |
| barriers_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_self_cw | -0.15 | 0.17 | [-0.51, 0.20] | 0.810 | [-0.11, 0.11] | 0.352 | 0.012 | Very Strong Evidence for Null | 1.000 | 32979 | 31122 |
| barriers_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_self_cw | 0.07 | 0.05 | [-0.03, 0.17] | 0.911 | [-0.11, 0.11] | 0.783 | 0.012 | Very Strong Evidence for Null | 1.000 | 52402 | 30949 |
| barriers_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_self_cw | 0.02 | 0.04 | [-0.05, 0.09] | 0.729 | [-0.11, 0.11] | 0.991 | 0.005 | Very Strong Evidence for Null | 1.000 | 69494 | 32479 |
| barriers_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_self_cw | -0.06 | 0.10 | [-0.27, 0.13] | 0.730 | [-0.11, 0.11] | 0.663 | 0.007 | Very Strong Evidence for Null | 1.000 | 38996 | 30433 |
| barriers_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_self_cw | 0.09 | 0.06 | [-0.02, 0.22] | 0.941 | [-0.11, 0.11] | 0.634 | 0.017 | Very Strong Evidence for Null | 1.000 | 37609 | 28398 |
| barriers_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Random Effects | |||||||||||
| sd(Intercept) | 0.61 | 0.08 | [0.48, 0.79] | NA | NA | NA | NA | NA | 1.000 | 12201 | 21564 |
| sd(persuasion_self_cw) | 0.04 | 0.03 | [0.00, 0.11] | NA | NA | NA | NA | NA | 1.000 | 16132 | 22554 |
| sd(persuasion_partner_cw) | 0.05 | 0.03 | [0.00, 0.12] | NA | NA | NA | NA | NA | 1.000 | 13197 | 18920 |
| sd(pressure_self_cw) | 0.07 | 0.06 | [0.00, 0.26] | NA | NA | NA | NA | NA | 1.000 | 23498 | 24276 |
| sd(pressure_partner_cw) | 0.08 | 0.07 | [0.00, 0.28] | NA | NA | NA | NA | NA | 1.000 | 18844 | 21409 |
| sd(pushing_self_cw) | 0.09 | 0.05 | [0.01, 0.20] | NA | NA | NA | NA | NA | 1.000 | 11728 | 13943 |
| sd(pushing_partner_cw) | 0.09 | 0.05 | [0.01, 0.21] | NA | NA | NA | NA | NA | 1.000 | 14414 | 16923 |
| sd(barriers_self_cw) | 0.33 | 0.05 | [0.24, 0.45] | NA | NA | NA | NA | NA | 1.000 | 30432 | 32326 |
| sd(barriers_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_self_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Additional Parameters | |||||||||||
| sigma | 0.84 | 0.02 | [0.81, 0.87] | NA | NA | NA | NA | NA | 1.000 | 61376 | 29276 |
plot(
bayestestR::p_direction(mood_gauss),
priors = TRUE
) +
coord_cartesian(xlim = c(-3, 3)) +
theme_bw()## Warning in `==.default`(dens$Parameter, parameter): longer object length
## is not a multiple of shorter object length
## Warning in is.na(e1) | is.na(e2): longer object length is not a multiple
## of shorter object length
## Possible multicollinearity between b_pressure_self_cb and
## b_persuasion_self_cb (r = 0.75), b_pressure_partner_cb and
## b_persuasion_self_cb (r = 0.72), b_pressure_self_cb and
## b_persuasion_partner_cb (r = 0.72), b_pressure_partner_cb and
## b_persuasion_partner_cb (r = 0.75), b_pushing_partner_cb and
## b_pushing_self_cb (r = 0.84). This might lead to inappropriate
## results. See 'Details' in '?rope'.
conditional_spaghetti(
mood_gauss,
effects = c('pushing_partner_cw'),
group_var = 'coupleID',
plot_full_range = TRUE
)$pushing_partner_cw
## [1] 0 5
df_double$reactance_ordinal <- factor(df_double$reactance,
levels = 0:5,
ordered = TRUE)
formula <- bf(
as.formula(
paste("reactance_ordinal", formula_terms)
)
, decomp = 'QR'
#, autocor = autocor_str
)
prior1 <- c(
brms::set_prior("normal(0, 2.5)", class = "b")
, brms::set_prior("normal(0, 2)", class = "sd", group = "coupleID", lb = 0)
)
#brms::validate_prior(
# prior1,
# formula = formula,
# data = df_double,
# family = cumulative() # HURDLE_CUMULATIVE
# )
#df_minimal <- df_double[, c("AorB", all.vars(as.formula(formula)))]
reactance_ordinal <- my_brm(
mi = use_mi,
imputed_data = implist,
formula = formula,
prior = prior1,
data = df_double,
family = brms::cumulative(),
#control = list(adapt_delta = 0.95),
iter = iterations,
warmup = warmup,
chains = 4,
cores = 4,
seed = 7777
, file = file.path("models_cache_brms", paste0("reactance_ordinal", suffix))
)## Warning: Rows containing NAs were excluded from the model.
if (check_models) {
check_brms(reactance_ordinal)
DHARMa.check_brms.all(reactance_ordinal, outliers_type = 'bootstrap')
}## # Check for Multicollinearity
##
## Low Correlation
##
## Term VIF VIF 95% CI Increased SE Tolerance
## pressure_self_cw 4.08 [3.86, 4.32] 2.02 0.25
## pressure_partner_cw 1.45 [1.39, 1.51] 1.20 0.69
## pushing_self_cw 1.23 [1.19, 1.29] 1.11 0.81
## pushing_partner_cw 1.18 [1.14, 1.23] 1.09 0.84
## persuasion_self_cb 1.07 [1.04, 1.12] 1.04 0.93
## persuasion_partner_cb 1.10 [1.07, 1.15] 1.05 0.91
## pressure_self_cb 1.29 [1.24, 1.34] 1.13 0.78
## pressure_partner_cb 1.28 [1.24, 1.34] 1.13 0.78
## pushing_self_cb 4.91 [4.63, 5.21] 2.22 0.20
## facilitators_self_cb 5.00 [4.71, 5.30] 2.24 0.20
## day 2.07 [1.97, 2.17] 1.44 0.48
## barriers_self_cw 2.35 [2.24, 2.48] 1.53 0.42
## Tolerance 95% CI
## [0.23, 0.26]
## [0.66, 0.72]
## [0.78, 0.84]
## [0.81, 0.87]
## [0.89, 0.96]
## [0.87, 0.94]
## [0.75, 0.81]
## [0.75, 0.81]
## [0.19, 0.22]
## [0.19, 0.21]
## [0.46, 0.51]
## [0.40, 0.45]
##
## Moderate Correlation
##
## Term VIF VIF 95% CI Increased SE Tolerance
## persuasion_self_cw 8.13 [7.65, 8.64] 2.85 0.12
## persuasion_partner_cw 9.88 [9.29, 10.51] 3.14 0.10
## pushing_partner_cb 6.22 [5.86, 6.61] 2.49 0.16
## barriers_self_cb 5.12 [4.83, 5.43] 2.26 0.20
## Tolerance 95% CI
## [0.12, 0.13]
## [0.10, 0.11]
## [0.15, 0.17]
## [0.18, 0.21]
## Error in h(simpleError(msg, call)) :
## error in evaluating the argument 'x' in selecting a method for function 'print': Predictive errors are not defined for ordinal or categorical models.
##
## Divergences:
## 0 of 40000 iterations ended with a divergence.
##
## Tree depth:
## 0 of 40000 iterations saturated the maximum tree depth of 10.
##
## Energy:
## E-BFMI indicated no pathological behavior.
## Using 10 posterior draws for ppc type 'ecdf_overlay' by default.
## Using 10 posterior draws for ppc type 'dens_overlay' by default.
## Warning: Found 33 observations with a pareto_k > 0.7 in model 'model'.
## We recommend to set 'moment_match = TRUE' in order to perform moment
## matching for problematic observations.
##
## DHARMa bootstrapped outlier test
##
## data: model.check
## outliers at both margin(s) = 1, observations = 486, p-value =
## 0.4
## alternative hypothesis: two.sided
## percent confidence interval:
## 0.000000000 0.002057613
## sample estimates:
## outlier frequency (expected: 0.000411522633744856 )
## 0.002057613
if (do_priorsense) {
gc()
priorsense::powerscale_sensitivity(reactance_ordinal, variable = priorsense_vars)
priorsense::powerscale_plot_dens(reactance_ordinal, variable = priorsense_vars)
priorsense::powerscale_plot_ecdf(reactance_ordinal, variable = priorsense_vars)
priorsense::powerscale_plot_quantities(reactance_ordinal, variable = priorsense_vars)
}summary_reactance_ordinal <- summarize_brms(
reactance_ordinal,
stats_to_report = stats_to_report,
rope_range = c(-0.18, 0.18),
model_rows_fixed = model_rows_fixed_ordinal,
model_rows_random = model_rows_random_ordinal,
model_rownames_fixed = model_rownames_fixed_ordinal,
model_rownames_random = model_rownames_random_ordinal,
exponentiate = T) ## Sampling priors, please wait...
===> warning: knot 3 removed - double knot ===> warning: knot 4 removed - double knot ===> warning: knot 5 removed - double knot * several double knots suggests that your data is strongly rounded, attention might be required possible infinite density at lower end running program with fewer knots ===> warning: knot 3 removed - double knot ===> warning: knot 4 removed - double knot ===> warning: knot 5 removed - double knot several double knots suggests that your data is strongly rounded, attention might be required * possible infinite density at lower end running program with fewer knots
## Warning in summarize_brms(reactance_ordinal, stats_to_report =
## stats_to_report, : Some rows from the model were omitted due to your
## provided model_rows_fixed or model_rows_random vectors. Missing rows:
## sd(persuasion_self_cw:barriers_self_cw),
## sd(pressure_self_cw:barriers_self_cw),
## sd(pushing_self_cw:barriers_self_cw),
## sd(persuasion_partner_cw:barriers_self_cw),
## sd(pressure_partner_cw:barriers_self_cw),
## sd(pushing_partner_cw:barriers_self_cw)
## Warning in summarize_brms(reactance_ordinal, stats_to_report =
## stats_to_report, : Length of model_rownames does not match number of
## rows
| OR | SE | 95% CI | pd | ROPE | inside ROPE | BF | BF_Evidence | Rhat | Bulk_ESS | Tail_ESS | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Intercept | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Intercept[1] | 4.62*** | 1.92 | [ 2.06, 10.96] | 1.000 | [0.84, 1.20] | 0.001 | 30.213 | Very Strong Evidence | 1.000 | 49636 | 35952 |
| Intercept[2] | 11.18*** | 4.82 | [ 4.87, 27.84] | 1.000 | [0.84, 1.20] | 0.000 | >100 | Overwhelming Evidence | 1.000 | 48764 | 34385 |
| Intercept[3] | 35.95*** | 16.93 | [ 14.79, 98.03] | 1.000 | [0.84, 1.20] | 0.000 | >100 | Overwhelming Evidence | 1.000 | 45655 | 32137 |
| Intercept[4] | 191.28*** | 107.60 | [ 67.26, 619.86] | 1.000 | [0.84, 1.20] | 0.000 | >100 | Overwhelming Evidence | 1.000 | 43599 | 32714 |
| Intercept[5] | 5962.77*** | 6286.89 | [965.89, 67535.08] | 1.000 | [0.84, 1.20] | 0.000 | >100 | Overwhelming Evidence | 1.000 | 53557 | 31040 |
| Within-Person Effects | |||||||||||
| persuasion_self_cw | 0.67** | 0.09 | [ 0.49, 0.87] | 0.998 | [0.84, 1.20] | 0.050 | 5.148 | Moderate Evidence | 1.000 | 38402 | 27272 |
| persuasion_partner_cw | 0.91 | 0.15 | [ 0.62, 1.24] | 0.720 | [0.84, 1.20] | 0.641 | 0.086 | Strong Evidence for Null | 1.000 | 37579 | 31837 |
| pressure_self_cw | 1.76 | 0.53 | [ 0.88, 3.27] | 0.950 | [0.84, 1.20] | 0.101 | 0.452 | Weak Evidence for Null | 1.000 | 36287 | 29812 |
| pressure_partner_cw | 1.22 | 0.48 | [ 0.46, 2.64] | 0.685 | [0.84, 1.20] | 0.299 | 0.105 | Moderate Evidence for Null | 1.000 | 36023 | 25749 |
| pushing_self_cw | 1.39* | 0.21 | [ 1.02, 1.89] | 0.980 | [0.84, 1.20] | 0.166 | 0.634 | Weak Evidence for Null | 1.000 | 43760 | 33120 |
| pushing_partner_cw | 0.93 | 0.18 | [ 0.63, 1.38] | 0.645 | [0.84, 1.20] | 0.613 | 0.075 | Strong Evidence for Null | 1.000 | 47812 | 32684 |
| day | 1.35 | 0.75 | [ 0.45, 4.02] | 0.708 | [0.84, 1.20] | 0.218 | 0.069 | Strong Evidence for Null | 1.000 | 59738 | 33884 |
| plan_selfPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| plan_partnerPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_self_cw | 1.00 | 0.41 | [ 0.44, 2.26] | 0.502 | [0.84, 1.20] | 0.343 | 0.073 | Strong Evidence for Null | 1.000 | 46807 | 34930 |
| barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Between-Person Effects | |||||||||||
| persuasion_self_cb | 1.46 | 1.25 | [ 0.26, 8.46] | 0.671 | [0.84, 1.20] | 0.149 | 0.097 | Strong Evidence for Null | 1.000 | 32017 | 31779 |
| persuasion_partner_cb | 1.81 | 1.73 | [ 0.29, 13.62] | 0.735 | [0.84, 1.20] | 0.125 | 0.108 | Moderate Evidence for Null | 1.000 | 32530 | 31009 |
| pressure_self_cb | 2.68 | 2.77 | [ 0.35, 22.07] | 0.826 | [0.84, 1.20] | 0.089 | 0.118 | Moderate Evidence for Null | 1.000 | 38087 | 35401 |
| pressure_partner_cb | 1.26 | 1.24 | [ 0.16, 8.36] | 0.594 | [0.84, 1.20] | 0.139 | 0.075 | Strong Evidence for Null | 1.000 | 32420 | 32304 |
| pushing_self_cb | 0.93 | 1.14 | [ 0.08, 11.41] | 0.521 | [0.84, 1.20] | 0.117 | 0.083 | Strong Evidence for Null | 1.000 | 33503 | 31761 |
| pushing_partner_cb | 0.02** | 0.03 | [ 0.00, 0.41] | 0.995 | [0.84, 1.20] | 0.004 | 2.465 | Weak Evidence | 1.000 | 35224 | 32193 |
| barriers_self_cb | 0.99 | 0.71 | [ 0.23, 4.07] | 0.506 | [0.84, 1.20] | 0.198 | 0.075 | Strong Evidence for Null | 1.000 | 47717 | 34334 |
| barriers_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cb | 0.80 | 0.35 | [ 0.34, 1.95] | 0.690 | [0.84, 1.20] | 0.280 | 0.107 | Moderate Evidence for Null | 1.000 | 43079 | 32459 |
| facilitators_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Interactions | |||||||||||
| persuasion_self_cw:barriers_self_cw | 0.72 | 0.15 | [ 0.46, 1.09] | 0.940 | [0.84, 1.20] | 0.234 | 0.289 | Moderate Evidence for Null | 1.000 | 46083 | 33103 |
| barriers_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_self_cw | 1.88 | 0.81 | [ 0.74, 4.55] | 0.919 | [0.84, 1.20] | 0.116 | 0.232 | Moderate Evidence for Null | 1.000 | 33935 | 30324 |
| barriers_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_self_cw | 0.78 | 0.19 | [ 0.45, 1.27] | 0.849 | [0.84, 1.20] | 0.347 | 0.124 | Moderate Evidence for Null | 1.000 | 40811 | 31072 |
| barriers_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_self_cw | 1.39 | 0.42 | [ 0.73, 2.67] | 0.860 | [0.84, 1.20] | 0.256 | 0.171 | Moderate Evidence for Null | 1.000 | 43165 | 30649 |
| barriers_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_self_cw | 0.88 | 0.60 | [ 0.22, 3.96] | 0.574 | [0.84, 1.20] | 0.201 | 0.098 | Strong Evidence for Null | 1.000 | 38959 | 30418 |
| barriers_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_self_cw | 1.36 | 0.48 | [ 0.68, 2.77] | 0.813 | [0.84, 1.20] | 0.273 | 0.118 | Moderate Evidence for Null | 1.000 | 51231 | 33221 |
| barriers_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Random Effects | |||||||||||
| sd(Intercept) | 1.22 | 0.32 | [0.69, 1.99] | NA | NA | NA | NA | NA | 1.000 | 18872 | 27617 |
| sd(persuasion_self_cw) | 0.33 | 0.22 | [0.02, 0.78] | NA | NA | NA | NA | NA | 1.000 | 10491 | 18771 |
| sd(persuasion_partner_cw) | 0.21 | 0.17 | [0.01, 0.64] | NA | NA | NA | NA | NA | 1.000 | 22296 | 24694 |
| sd(pressure_self_cw) | 0.81 | 0.42 | [0.12, 1.86] | NA | NA | NA | NA | NA | 1.000 | 13988 | 15164 |
| sd(pressure_partner_cw) | 0.56 | 0.49 | [0.02, 2.07] | NA | NA | NA | NA | NA | 1.000 | 17825 | 24858 |
| sd(pushing_self_cw) | 0.31 | 0.23 | [0.02, 0.83] | NA | NA | NA | NA | NA | 1.000 | 12985 | 21502 |
| sd(pushing_partner_cw) | 0.24 | 0.21 | [0.01, 0.87] | NA | NA | NA | NA | NA | 1.000 | 20012 | 26071 |
| sd(barriers_self_cw) | 1.03 | 0.50 | [0.11, 2.07] | NA | NA | NA | NA | NA | 1.000 | 14688 | 15119 |
| sd(barriers_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_self_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Additional Parameters | |||||||||||
| sigma | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| disc | 1.00 | 0.00 | [1.00, 1.00] | NA | NA | NA | NA | NA | NA | NA | NA |
plot(
bayestestR::p_direction(reactance_ordinal),
priors = TRUE
) +
coord_cartesian(xlim = c(-6, 6)) +
theme_bw()## Warning in `==.default`(dens$Parameter, parameter): longer object length
## is not a multiple of shorter object length
## Warning in is.na(e1) | is.na(e2): longer object length is not a multiple
## of shorter object length
## Possible multicollinearity between b_Intercept[4] and
## b_Intercept[2] (r = 0.79), b_Intercept[4] and b_Intercept[3] (r =
## 0.85), b_pressure_partner_cb and b_persuasion_partner_cb (r =
## 0.77). This might lead to inappropriate results. See 'Details' in
## '?rope'.
introduce_binary_reactance <- function(data) {
data$is_reactance <- factor(data$reactance > 0, levels = c(FALSE, TRUE), labels = c(0, 1))
return(data)
}
df_double <- introduce_binary_reactance(df_double)
if (use_mi) {
for (i in seq_along(implist)) {
implist[[i]] <- introduce_binary_reactance(implist[[i]])
}
}
formula <- bf(
as.formula(
paste("is_reactance", formula_terms)
)
, decomp = 'QR'
#, autocor = autocor_str
)
prior1 <- c(
brms::set_prior("normal(0, 2.5)", class = "b")
, brms::set_prior("normal(0, 10)", class = "Intercept", lb=0, ub=5)
, brms::set_prior("normal(0, 2)", class = "sd", group = "coupleID", lb = 0)
)
#brms::validate_prior(
# prior1,
# formula = formula,
# data = df_double,
# family = bernoulli()
# )
#df_minimal <- df_double[, c("AorB", all.vars(as.formula(formula)))]
is_reactance <- my_brm(
mi = use_mi,
imputed_data = implist,
formula = formula,
prior = prior1,
data = df_double,
family = brms::bernoulli(),
#control = list(adapt_delta = 0.95, max_treedepth = 15),
iter = iterations,
warmup = warmup,
chains = 4,
cores = 4,
seed = 7777,
file = file.path("models_cache_brms", paste0("is_reactance", suffix))
#, file_refit = 'always'
)## Warning: Rows containing NAs were excluded from the model.
## # Check for Multicollinearity
##
## Low Correlation
##
## Term VIF VIF 95% CI Increased SE Tolerance
## persuasion_self_cw 1.11 [1.08, 1.16] 1.05 0.90
## persuasion_partner_cw 1.25 [1.20, 1.30] 1.12 0.80
## pressure_self_cw 1.04 [1.02, 1.10] 1.02 0.96
## pressure_partner_cw 1.05 [1.03, 1.10] 1.03 0.95
## pushing_self_cw 1.11 [1.08, 1.16] 1.06 0.90
## pushing_partner_cw 1.33 [1.28, 1.38] 1.15 0.75
## persuasion_self_cb 3.66 [3.46, 3.87] 1.91 0.27
## persuasion_partner_cb 3.82 [3.62, 4.04] 1.95 0.26
## pressure_self_cb 2.35 [2.24, 2.47] 1.53 0.43
## pressure_partner_cb 2.27 [2.17, 2.39] 1.51 0.44
## pushing_self_cb 2.35 [2.24, 2.48] 1.53 0.43
## pushing_partner_cb 2.30 [2.19, 2.42] 1.52 0.44
## barriers_self_cb 1.24 [1.19, 1.29] 1.11 0.81
## facilitators_self_cb 1.08 [1.05, 1.12] 1.04 0.93
## day 1.05 [1.03, 1.10] 1.03 0.95
## barriers_self_cw 1.40 [1.34, 1.46] 1.18 0.72
## Tolerance 95% CI
## [0.86, 0.93]
## [0.77, 0.83]
## [0.91, 0.98]
## [0.91, 0.97]
## [0.86, 0.93]
## [0.72, 0.78]
## [0.26, 0.29]
## [0.25, 0.28]
## [0.40, 0.45]
## [0.42, 0.46]
## [0.40, 0.45]
## [0.41, 0.46]
## [0.78, 0.84]
## [0.89, 0.95]
## [0.91, 0.97]
## [0.69, 0.74]
## # Distribution of Model Family
##
## Predicted Distribution of Residuals
##
## Distribution Probability
## normal 31%
## beta 19%
## cauchy 19%
##
## Predicted Distribution of Response
##
## Distribution Probability
## bernoulli 75%
## beta-binomial 16%
## binomial 9%
##
## Divergences:
## 0 of 40000 iterations ended with a divergence.
##
## Tree depth:
## 0 of 40000 iterations saturated the maximum tree depth of 10.
##
## Energy:
## E-BFMI indicated no pathological behavior.
## Using 10 posterior draws for ppc type 'ecdf_overlay' by default.
## Using 10 posterior draws for ppc type 'dens_overlay' by default.
## Warning: Found 96 observations with a pareto_k > 0.7 in model 'model'.
## We recommend to set 'moment_match = TRUE' in order to perform moment
## matching for problematic observations.
##
## DHARMa outlier test based on exact binomial test with
## approximate expectations
##
## data: model.check
## outliers at both margin(s) = 0, observations = 486, p-value = 1
## alternative hypothesis: true probability of success is not equal to 0.001998002
## 95 percent confidence interval:
## 0.000000000 0.007561553
## sample estimates:
## frequency of outliers (expected: 0.001998001998002 )
## 0
if (do_priorsense) {
gc()
priorsense::powerscale_sensitivity(is_reactance, variable = priorsense_vars)
priorsense::powerscale_plot_dens(is_reactance, variable = priorsense_vars)
priorsense::powerscale_plot_ecdf(is_reactance, variable = priorsense_vars)
priorsense::powerscale_plot_quantities(is_reactance, variable = priorsense_vars)
}summary_is_reactance <- summarize_brms(
is_reactance,
stats_to_report = stats_to_report,
model_rows_fixed = model_rows_fixed,
model_rows_random = model_rows_random,
model_rownames_fixed = model_rownames_fixed,
model_rownames_random = model_rownames_random,
exponentiate = T) ## Sampling priors, please wait...
## Warning in summarize_brms(is_reactance, stats_to_report =
## stats_to_report, : Some rows from the model were omitted due to your
## provided model_rows_fixed or model_rows_random vectors. Missing rows:
## sd(persuasion_self_cw:barriers_self_cw),
## sd(pressure_self_cw:barriers_self_cw),
## sd(pushing_self_cw:barriers_self_cw),
## sd(persuasion_partner_cw:barriers_self_cw),
## sd(pressure_partner_cw:barriers_self_cw),
## sd(pushing_partner_cw:barriers_self_cw)
## Warning in summarize_brms(is_reactance, stats_to_report =
## stats_to_report, : Length of model_rownames does not match number of
## rows
| OR | SE | 95% CI | pd | ROPE | inside ROPE | BF | BF_Evidence | Rhat | Bulk_ESS | Tail_ESS | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Intercept | 0.47 | 0.24 | [0.16, 1.34] | 0.924 | [0.83, 1.20] | 0.095 | 0.253 | Moderate Evidence for Null | 1.000 | 33627 | 33018 |
| Within-Person Effects | |||||||||||
| persuasion_self_cw | 0.63* | 0.14 | [0.38, 0.95] | 0.986 | [0.83, 1.20] | 0.084 | 1.396 | Weak Evidence | 1.000 | 28023 | 28635 |
| persuasion_partner_cw | 1.07 | 0.32 | [0.60, 2.14] | 0.596 | [0.83, 1.20] | 0.453 | 0.132 | Moderate Evidence for Null | 1.000 | 24199 | 24283 |
| pressure_self_cw | 4.29* | 3.57 | [1.00, 32.57] | 0.975 | [0.83, 1.20] | 0.028 | 1.590 | Weak Evidence | 1.000 | 22611 | 23694 |
| pressure_partner_cw | 1.64 | 1.47 | [0.26, 16.69] | 0.716 | [0.83, 1.20] | 0.142 | 0.223 | Moderate Evidence for Null | 1.000 | 27214 | 25172 |
| pushing_self_cw | 1.70* | 0.42 | [1.10, 3.13] | 0.991 | [0.83, 1.20] | 0.060 | 1.632 | Weak Evidence | 1.000 | 22475 | 26993 |
| pushing_partner_cw | 0.83 | 0.30 | [0.40, 1.85] | 0.699 | [0.83, 1.20] | 0.335 | 0.157 | Moderate Evidence for Null | 1.000 | 30415 | 26455 |
| day | 1.42 | 1.01 | [0.34, 5.70] | 0.690 | [0.83, 1.20] | 0.178 | 0.087 | Strong Evidence for Null | 1.000 | 49157 | 32314 |
| plan_selfPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| plan_partnerPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_self_cw | 0.82 | 0.48 | [0.25, 2.82] | 0.633 | [0.83, 1.20] | 0.228 | 0.114 | Moderate Evidence for Null | 1.000 | 37379 | 32322 |
| barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Between-Person Effects | |||||||||||
| persuasion_self_cb | 4.16 | 5.95 | [0.25, 90.18] | 0.844 | [0.83, 1.20] | 0.061 | 0.246 | Moderate Evidence for Null | 1.000 | 18736 | 24685 |
| persuasion_partner_cb | 7.65 | 11.79 | [0.42, 218.29] | 0.914 | [0.83, 1.20] | 0.040 | 0.344 | Weak Evidence for Null | 1.000 | 18245 | 24902 |
| pressure_self_cb | 68.56 | 167.69 | [0.81, 13217.49] | 0.969 | [0.83, 1.20] | 0.012 | 0.881 | Weak Evidence for Null | 1.000 | 23568 | 27135 |
| pressure_partner_cb | 0.65 | 1.76 | [0.00, 111.32] | 0.562 | [0.83, 1.20] | 0.054 | 0.202 | Moderate Evidence for Null | 1.000 | 17143 | 26302 |
| pushing_self_cb | 0.81 | 1.77 | [0.01, 59.15] | 0.537 | [0.83, 1.20] | 0.065 | 0.150 | Moderate Evidence for Null | 1.000 | 20753 | 27025 |
| pushing_partner_cb | 0.01* | 0.02 | [0.00, 0.70] | 0.983 | [0.83, 1.20] | 0.007 | 1.449 | Weak Evidence | 1.000 | 20611 | 27523 |
| barriers_self_cb | 0.67 | 0.75 | [0.07, 5.80] | 0.638 | [0.83, 1.20] | 0.120 | 0.123 | Moderate Evidence for Null | 1.000 | 32817 | 31595 |
| barriers_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cb | 0.99 | 0.66 | [0.26, 3.96] | 0.508 | [0.83, 1.20] | 0.212 | 0.144 | Moderate Evidence for Null | 1.000 | 26899 | 29198 |
| facilitators_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Interactions | |||||||||||
| persuasion_self_cw:barriers_self_cw | 0.93 | 0.26 | [0.51, 1.65] | 0.601 | [0.83, 1.20] | 0.462 | 0.120 | Moderate Evidence for Null | 1.000 | 37266 | 31546 |
| barriers_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_self_cw | 1.71 | 1.47 | [0.27, 11.16] | 0.735 | [0.83, 1.20] | 0.137 | 0.188 | Moderate Evidence for Null | 1.000 | 27968 | 29099 |
| barriers_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_self_cw | 0.67 | 0.28 | [0.26, 1.47] | 0.845 | [0.83, 1.20] | 0.223 | 0.202 | Moderate Evidence for Null | 1.000 | 29742 | 27471 |
| barriers_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_self_cw | 1.37 | 0.70 | [0.46, 4.36] | 0.734 | [0.83, 1.20] | 0.228 | 0.182 | Moderate Evidence for Null | 1.000 | 30625 | 27331 |
| barriers_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_self_cw | 0.86 | 1.18 | [0.05, 17.62] | 0.546 | [0.83, 1.20] | 0.107 | 0.193 | Moderate Evidence for Null | 1.000 | 30311 | 28639 |
| barriers_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_self_cw | 1.76 | 0.97 | [0.59, 5.63] | 0.847 | [0.83, 1.20] | 0.154 | 0.211 | Moderate Evidence for Null | 1.000 | 40322 | 30462 |
| barriers_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Random Effects | |||||||||||
| sd(Intercept) | 2.49 | 0.57 | [1.54, 3.87] | NA | NA | NA | NA | NA | 1.001 | 13566 | 23976 |
| sd(persuasion_self_cw) | 0.68 | 0.31 | [0.08, 1.39] | NA | NA | NA | NA | NA | 1.001 | 6918 | 8734 |
| sd(persuasion_partner_cw) | 0.76 | 0.44 | [0.07, 1.83] | NA | NA | NA | NA | NA | 1.000 | 10555 | 14198 |
| sd(pressure_self_cw) | 2.41 | 0.92 | [0.87, 4.59] | NA | NA | NA | NA | NA | 1.000 | 15602 | 15620 |
| sd(pressure_partner_cw) | 1.84 | 1.20 | [0.13, 4.57] | NA | NA | NA | NA | NA | 1.000 | 14595 | 15886 |
| sd(pushing_self_cw) | 0.62 | 0.36 | [0.05, 1.47] | NA | NA | NA | NA | NA | 1.000 | 9022 | 12138 |
| sd(pushing_partner_cw) | 0.51 | 0.43 | [0.02, 1.72] | NA | NA | NA | NA | NA | 1.000 | 13904 | 21185 |
| sd(barriers_self_cw) | 1.52 | 0.67 | [0.24, 2.97] | NA | NA | NA | NA | NA | 1.000 | 11717 | 10547 |
| sd(barriers_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_self_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Additional Parameters | |||||||||||
| sigma | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
plot(
bayestestR::p_direction(is_reactance),
priors = TRUE
) +
coord_cartesian(xlim = c(-6, 6)) +
theme_bw()## Warning in `==.default`(dens$Parameter, parameter): longer object length
## is not a multiple of shorter object length
## Warning in is.na(e1) | is.na(e2): longer object length is not a multiple
## of shorter object length
## Possible multicollinearity between b_persuasion_partner_cb and
## b_persuasion_self_cb (r = 0.72). This might lead to inappropriate
## results. See 'Details' in '?rope'.
conditional_spaghetti(
is_reactance,
effects = c('pressure_self_cw', 'pushing_self_cw'),
group_var = 'coupleID',
plot_full_range = TRUE
)\(pressure_self_cw
<img
src="07_SensitivityBarriersFacilitatorsInteract_files/figure-html/report_is_reactance-3.png"
width="2400" />\)pushing_self_cw
## Hypothesis Tests for class b:
## Hypothesis Estimate Est.Error CI.Lower CI.Upper
## 1 (exp(pressure_sel... > 0 5.59 13.16 -0.74 20.62
## Evid.Ratio Post.Prob Star
## 1 6.48 0.87
## ---
## 'CI': 90%-CI for one-sided and 95%-CI for two-sided hypotheses.
## '*': For one-sided hypotheses, the posterior probability exceeds 95%;
## for two-sided hypotheses, the value tested against lies outside the 95%-CI.
## Posterior probabilities of point hypotheses assume equal prior probabilities.
summary_all_models <- report_side_by_side(
pa_sub,
pa_obj_log,
mood_gauss,
is_reactance,
stats_to_report = c('CI'),
model_rows_random = model_rows_random,
model_rows_fixed = model_rows_fixed,
model_rownames_random = model_rownames_random,
model_rownames_fixed = model_rownames_fixed
)[1] “pa_sub”
## Warning in summarize_brms(model, exponentiate = exponentiate,
## stats_to_report = stats_to_report, : Coefficients were exponentiated.
## Double check if this was intended.
## Warning in summarize_brms(model, exponentiate = exponentiate,
## stats_to_report = stats_to_report, : Some rows from the model were
## omitted due to your provided model_rows_fixed or model_rows_random
## vectors. Missing rows: sd(persuasion_partner_cw:barriers_self_cw),
## sd(persuasion_self_cw:barriers_self_cw),
## sd(pressure_partner_cw:barriers_self_cw),
## sd(pressure_self_cw:barriers_self_cw),
## sd(pushing_partner_cw:barriers_self_cw),
## sd(pushing_self_cw:barriers_self_cw)
## Warning in summarize_brms(model, exponentiate = exponentiate,
## stats_to_report = stats_to_report, : Length of model_rownames does not
## match number of rows
[1] “pa_obj_log”
## Warning in summarize_brms(model, exponentiate = exponentiate,
## stats_to_report = stats_to_report, : Coefficients were exponentiated.
## Double check if this was intended.
## Warning in summarize_brms(model, exponentiate = exponentiate,
## stats_to_report = stats_to_report, : Some rows from the model were
## omitted due to your provided model_rows_fixed or model_rows_random
## vectors. Missing rows: sd(persuasion_self_cw:barriers_self_cw),
## sd(pressure_self_cw:barriers_self_cw),
## sd(pushing_self_cw:barriers_self_cw),
## sd(persuasion_partner_cw:barriers_self_cw),
## sd(pressure_partner_cw:barriers_self_cw),
## sd(pushing_partner_cw:barriers_self_cw)
## Warning in summarize_brms(model, exponentiate = exponentiate,
## stats_to_report = stats_to_report, : Length of model_rownames does not
## match number of rows
[1] “mood_gauss”
## Warning in summarize_brms(model, exponentiate = exponentiate,
## stats_to_report = stats_to_report, : Some rows from the model were
## omitted due to your provided model_rows_fixed or model_rows_random
## vectors. Missing rows: sd(persuasion_self_cw:barriers_self_cw),
## sd(pressure_self_cw:barriers_self_cw),
## sd(pushing_self_cw:barriers_self_cw),
## sd(persuasion_partner_cw:barriers_self_cw),
## sd(pressure_partner_cw:barriers_self_cw),
## sd(pushing_partner_cw:barriers_self_cw)
## Warning in summarize_brms(model, exponentiate = exponentiate,
## stats_to_report = stats_to_report, : Length of model_rownames does not
## match number of rows
[1] “is_reactance”
## Warning in summarize_brms(model, exponentiate = exponentiate,
## stats_to_report = stats_to_report, : Some rows from the model were
## omitted due to your provided model_rows_fixed or model_rows_random
## vectors. Missing rows: sd(persuasion_self_cw:barriers_self_cw),
## sd(pressure_self_cw:barriers_self_cw),
## sd(pushing_self_cw:barriers_self_cw),
## sd(persuasion_partner_cw:barriers_self_cw),
## sd(pressure_partner_cw:barriers_self_cw),
## sd(pushing_partner_cw:barriers_self_cw)
## Warning in summarize_brms(model, exponentiate = exponentiate,
## stats_to_report = stats_to_report, : Length of model_rownames does not
## match number of rows
summary_all_models <- summary_all_models %>%
print_df(
rows_to_pack = rows_to_pack
) %>%
add_header_above(
c(
" ", "Hurdle Component" = 2, "Non-Zero Component" = 2,
" " = 6
)
) %>%
add_header_above(
c(" ", "Subjective MVPA Hurdle Lognormal" = 4,
"Device-Based MVPA Log (Gaussian)" = 2,
"Mood Gaussian" = 2,
#"Reactance Ordinal" = 2,
"Reactance Dichotome" = 2
)
)
export_xlsx(
summary_all_models,
rows_to_pack = rows_to_pack,
file.path("Output", paste0("AllModels", suffix, ".xlsx")),
merge_option = 'both',
simplify_2nd_row = FALSE,
line_above_rows = c(1,2),
line_below_rows = c(-1)
)
summary_all_models| exp(Est.)_hu pa_sub | 95% CI_hu pa_sub | exp(Est.)_nonzero pa_sub | 95% CI_nonzero pa_sub | exp(Est.) pa_obj_log | 95% CI pa_obj_log | Est. mood_gauss | 95% CI mood_gauss | OR is_reactance | 95% CI is_reactance | |
|---|---|---|---|---|---|---|---|---|---|---|
| Intercept | 2.89*** | [ 1.62, 5.14] | 49.15*** | [41.78, 58.06] | 122.92*** | [108.77, 138.83] | 3.80*** | [ 3.59, 4.02] | 0.47 | [0.16, 1.34] |
| Within-Person Effects | ||||||||||
| persuasion_self_cw | 1.61*** | [ 1.30, 2.07] | 1.04 | [ 0.99, 1.10] | 1.03 | [ 0.99, 1.06] | 0.01 | [-0.03, 0.06] | 0.63* | [0.38, 0.95] |
| persuasion_partner_cw | 1.44*** | [ 1.17, 1.86] | 1.02 | [ 0.98, 1.07] | 1.03 | [ 0.99, 1.07] | 0.01 | [-0.04, 0.06] | 1.07 | [0.60, 2.14] |
| pressure_self_cw | 0.84 | [ 0.43, 1.92] | 0.90 | [ 0.78, 1.03] | 0.95 | [ 0.85, 1.05] | -0.02 | [-0.16, 0.11] | 4.29* | [1.00, 32.57] |
| pressure_partner_cw | 1.64 | [ 0.85, 5.26] | 0.96 | [ 0.86, 1.06] | 0.98 | [ 0.90, 1.06] | -0.04 | [-0.17, 0.08] | 1.64 | [0.26, 16.69] |
| pushing_self_cw | 1.22 | [ 0.82, 1.84] | 0.98 | [ 0.92, 1.05] | 1.03 | [ 0.97, 1.08] | 0.02 | [-0.06, 0.10] | 1.70* | [1.10, 3.13] |
| pushing_partner_cw | 1.60* | [ 1.07, 2.78] | 0.96 | [ 0.90, 1.02] | 0.99 | [ 0.94, 1.04] | 0.08 | [ 0.00, 0.15] | 0.83 | [0.40, 1.85] |
| day | 0.88 | [ 0.54, 1.42] | 1.03 | [ 0.89, 1.18] | 0.97 | [ 0.88, 1.07] | 0.25** | [ 0.10, 0.39] | 1.42 | [0.34, 5.70] |
| plan_selfPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| plan_partnerPlan | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_self_cw | 0.68 | [ 0.42, 1.12] | 1.08 | [ 0.97, 1.20] | 0.97 | [ 0.91, 1.03] | -0.26*** | [-0.38, -0.12] | 0.82 | [0.25, 2.82] |
| barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cw | NA | NA | NA | NA | 1.00*** | [ 1.00, 1.00] | NA | NA | NA | NA |
| Between-Person Effects | ||||||||||
| persuasion_self_cb | 0.91 | [ 0.25, 3.09] | 1.07 | [ 0.76, 1.50] | 0.96 | [ 0.69, 1.33] | 0.07 | [-0.52, 0.63] | 4.16 | [0.25, 90.18] |
| persuasion_partner_cb | 1.35 | [ 0.38, 4.59] | 0.94 | [ 0.67, 1.31] | 0.82 | [ 0.59, 1.15] | 0.33 | [-0.25, 0.89] | 7.65 | [0.42, 218.29] |
| pressure_self_cb | 0.23 | [ 0.04, 1.24] | 0.69 | [ 0.31, 1.59] | 1.16 | [ 0.81, 1.67] | -0.02 | [-0.59, 0.56] | 68.56 | [0.81, 13217.49] |
| pressure_partner_cb | 0.20 | [ 0.03, 1.03] | 0.51 | [ 0.23, 1.17] | 1.06 | [ 0.75, 1.51] | -0.27 | [-0.83, 0.31] | 0.65 | [0.00, 111.32] |
| pushing_self_cb | 1.35 | [ 0.23, 7.96] | 1.50 | [ 0.83, 2.70] | 1.14 | [ 0.70, 1.82] | 0.22 | [-0.61, 1.04] | 0.81 | [0.01, 59.15] |
| pushing_partner_cb | 1.76 | [ 0.30, 10.33] | 1.65 | [ 0.91, 2.95] | 1.29 | [ 0.81, 2.06] | 0.01 | [-0.82, 0.82] | 0.01* | [0.00, 0.70] |
| barriers_self_cb | 0.50** | [ 0.30, 0.83] | 0.92 | [ 0.78, 1.09] | 0.78*** | [ 0.70, 0.87] | -0.57*** | [-0.72, -0.41] | 0.67 | [0.07, 5.80] |
| barriers_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cb | 1.20 | [ 0.82, 1.77] | 1.14* | [ 1.03, 1.27] | 0.97 | [ 0.89, 1.05] | 0.32*** | [ 0.21, 0.44] | 0.99 | [0.26, 3.96] |
| facilitators_partner_cb | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| weartime_self_cb | NA | NA | NA | NA | 1.00* | [ 1.00, 1.00] | NA | NA | NA | NA |
| Interactions | ||||||||||
| persuasion_self_cw:barriers_self_cw | 0.95 | [ 0.62, 1.46] | 0.99 | [ 0.92, 1.07] | 0.96 | [ 0.92, 1.01] | -0.01 | [-0.09, 0.06] | 0.93 | [0.51, 1.65] |
| barriers_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_self_cw | 0.49 | [ 0.15, 1.54] | 1.02 | [ 0.79, 1.31] | 1.05 | [ 0.89, 1.26] | -0.15 | [-0.51, 0.20] | 1.71 | [0.27, 11.16] |
| barriers_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_self_cw | 1.94 | [ 0.99, 4.10] | 0.96 | [ 0.86, 1.07] | 0.98 | [ 0.91, 1.05] | 0.07 | [-0.03, 0.17] | 0.67 | [0.26, 1.47] |
| barriers_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_self_cw | 0.68* | [ 0.46, 0.95] | 1.06 | [ 0.99, 1.13] | 1.03 | [ 0.98, 1.09] | 0.02 | [-0.05, 0.09] | 1.37 | [0.46, 4.36] |
| barriers_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_self_cw | 0.82 | [ 0.26, 2.53] | 0.90 | [ 0.75, 1.05] | 0.97 | [ 0.85, 1.10] | -0.06 | [-0.27, 0.13] | 0.86 | [0.05, 17.62] |
| barriers_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_self_cw | 1.71 | [ 0.99, 3.43] | 1.05 | [ 0.95, 1.18] | 1.07 | [ 0.99, 1.16] | 0.09 | [-0.02, 0.22] | 1.76 | [0.59, 5.63] |
| barriers_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_self_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_self_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_self_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:barriers_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| barriers_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| persuasion_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:persuasion_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pressure_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pressure_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| pushing_partner_cw:facilitators_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| facilitators_partner_cw:pushing_partner_cw | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Random Effects | ||||||||||
| sd(Intercept) | 1.44 | [1.08, 1.97] | 0.31 | [0.23, 0.42] | 0.33 | [0.25, 0.43] | 0.61 | [0.48, 0.79] | 2.49 | [1.54, 3.87] |
| sd(persuasion_self_cw) | 0.17 | [0.01, 0.51] | 0.10 | [0.05, 0.16] | 0.06 | [0.02, 0.10] | 0.04 | [0.00, 0.11] | 0.68 | [0.08, 1.39] |
| sd(persuasion_partner_cw) | 0.20 | [0.01, 0.54] | 0.05 | [0.01, 0.11] | 0.05 | [0.01, 0.10] | 0.05 | [0.00, 0.12] | 0.76 | [0.07, 1.83] |
| sd(pressure_self_cw) | 0.54 | [0.03, 2.05] | 0.08 | [0.00, 0.30] | 0.07 | [0.00, 0.24] | 0.07 | [0.00, 0.26] | 2.41 | [0.87, 4.59] |
| sd(pressure_partner_cw) | 0.53 | [0.03, 2.08] | 0.05 | [0.00, 0.20] | 0.04 | [0.00, 0.13] | 0.08 | [0.00, 0.28] | 1.84 | [0.13, 4.57] |
| sd(pushing_self_cw) | 0.61 | [0.07, 1.30] | 0.07 | [0.00, 0.16] | 0.08 | [0.01, 0.15] | 0.09 | [0.01, 0.20] | 0.62 | [0.05, 1.47] |
| sd(pushing_partner_cw) | 0.64 | [0.07, 1.47] | 0.06 | [0.00, 0.15] | 0.05 | [0.00, 0.11] | 0.09 | [0.01, 0.21] | 0.51 | [0.02, 1.72] |
| sd(barriers_self_cw) | 1.27 | [0.91, 1.79] | 0.20 | [0.08, 0.33] | 0.14 | [0.08, 0.21] | 0.33 | [0.24, 0.45] | 1.52 | [0.24, 2.97] |
| sd(barriers_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_self_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| sd(facilitators_partner_cw) | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Additional Parameters | ||||||||||
| sigma | NA | NA | 0.66 | [0.63, 0.69] | 0.53 | [0.51, 0.55] | 0.84 | [0.81, 0.87] | NA | NA |
Plot Interaction effect.
library(ggplot2)
library(plotly)
p <- conditional_effects(
pa_sub,
dpar = 'hu',
effects = 'pushing_self_cw:barriers_self_cw',
re_formula = NA,
method = 'posterior_linpred',
plot = FALSE
)
p2 <- p
p2[[1]]$estimate__ <- 1 - p[[1]]$estimate__
p2[[1]]$lower__ <- 1 - p[[1]]$upper__
p2[[1]]$upper__ <- 1 - p[[1]]$lower__
plots <- plot(p2, theme = theme_minimal(), plot = FALSE)
plots[[1]] +
scale_color_manual(values = c("steelblue", "forestgreen", "coral")) +
scale_fill_manual(values = c("steelblue", "forestgreen", "coral"))library(tidybayes)
library(dplyr)
library(ggplot2)
plot_slope_by_moderator <- function(
mod,
df,
moderator,
predictor_par,
interaction_par,
exponentiate = FALSE,
n_points = 1000,
fill_colors = c("Significant" = "steelblue",
"Non-significant" = "coral"),
line_colors = fill_colors, # Reuse fill colors by default
vjust_val = -1.5
) {
# Generate a sequence of moderator values
moderator_seq <- seq(
from = min(df[[moderator]], na.rm = TRUE),
to = max(df[[moderator]], na.rm = TRUE),
length.out = n_points
)
# Extract posterior draws for the parameters of interest
library(rlang)
predictor_sym <- rlang::sym(predictor_par)
interaction_sym <- rlang::sym(interaction_par)
post_draws <- mod %>%
spread_draws(!!predictor_sym, !!interaction_sym)
# For each moderator value, compute the slope for each posterior draw
slope_list <- lapply(moderator_seq, function(mod_val) {
tibble(
moderator_value = mod_val,
slope = - (post_draws[[predictor_par]] + mod_val * post_draws[[interaction_par]])
)
})
# Combine the list into a single data frame
slope_df <- bind_rows(slope_list)
# Summarize the posterior for each moderator value (using a 95% credible interval)
slope_summary <- slope_df %>%
group_by(moderator_value) %>%
summarize(
slope_median = median(slope),
slope_lower = quantile(slope, probs = 0.025),
slope_upper = quantile(slope, probs = 0.975)
) %>%
# Create significance flag: "sig" if CI excludes 0, "ns" otherwise
mutate(sig_flag = if_else(slope_lower > 0 | slope_upper < 0, "sig", "ns")) %>%
arrange(moderator_value)
# If exponentiate == TRUE, transform slope columns
if (exponentiate) {
slope_summary <- slope_summary %>%
mutate(
slope_median_exp = exp(slope_median),
slope_lower_exp = exp(slope_lower),
slope_upper_exp = exp(slope_upper)
)
}
# Identify boundary rows and duplicate them for each category
slope_summary <- slope_summary %>%
mutate(
next_sig_flag = lead(sig_flag),
is_boundary = sig_flag != next_sig_flag & !is.na(next_sig_flag)
)
boundary_rows <- slope_summary %>%
filter(is_boundary)
boundary_rows_next <- boundary_rows
boundary_rows_next$sig_flag <- boundary_rows_next$next_sig_flag
slope_summary_extended <- bind_rows(slope_summary, boundary_rows_next)
# Split into "sig" and "ns"
slope_summary_sig <- slope_summary_extended %>% filter(sig_flag == "sig")
slope_summary_ns <- slope_summary_extended %>% filter(sig_flag == "ns")
# Build the base plot:
# We'll use either slope_{median, lower, upper} or slope_{median_exp, lower_exp, upper_exp}
# depending on exponentiate.
if (exponentiate) {
median_col <- "slope_median_exp"
lower_col <- "slope_lower_exp"
upper_col <- "slope_upper_exp"
y_lab <- "Odds Ratio (Exponentiated Slope)"
ref_line <- 1 # reference line for ORs is 1
} else {
median_col <- "slope_median"
lower_col <- "slope_lower"
upper_col <- "slope_upper"
y_lab <- "Slope (Log-Odds Scale)"
ref_line <- 0
}
p <- ggplot() +
# Non-significant region
geom_ribbon(
data = slope_summary_ns,
aes_string(
x = "moderator_value",
ymin = lower_col,
ymax = upper_col,
fill = '"Non-significant"'
),
alpha = 0.2
) +
geom_line(
data = slope_summary_ns,
aes_string(
x = "moderator_value",
y = median_col,
color = '"Non-significant"'
),
size = 1
) +
# Significant region
geom_ribbon(
data = slope_summary_sig,
aes_string(
x = "moderator_value",
ymin = lower_col,
ymax = upper_col,
fill = '"Significant"'
),
alpha = 0.2
) +
geom_line(
data = slope_summary_sig,
aes_string(
x = "moderator_value",
y = median_col,
color = '"Significant"'
),
size = 1
) +
# Reference line (0 for log-odds, 1 for odds-ratios)
geom_hline(
yintercept = ref_line,
linetype = "dashed"
) +
# Manual scales for fill & color
scale_fill_manual(
values = fill_colors
) +
scale_color_manual(
values = line_colors
) +
labs(
x = moderator,
y = y_lab,
fill = "Significance",
color = "Significance"
) +
theme_minimal()
# Add boundary lines (where significance changes) & labels
p2 <- p +
geom_vline(
data = boundary_rows,
aes(xintercept = moderator_value),
color = fill_colors["Significant"],
alpha = 0.35,
size = 0.7,
linetype = "dashed"
) +
geom_text(
data = boundary_rows,
aes(x = moderator_value, y = -Inf, label = round(moderator_value, 3)),
vjust = vjust_val,
size = 3.7
)
return(p2)
}
p_log_odds <- plot_slope_by_moderator(
mod = pa_sub,
df = df_double,
moderator = "barriers_self_cw",
predictor_par = "b_hu_pushing_self_cw",
interaction_par = "b_hu_pushing_self_cw:barriers_self_cw",
exponentiate = FALSE
)
p_log_oddsp_odds_ratio <- plot_slope_by_moderator(
mod = pa_sub,
df = df_double,
moderator = "barriers_self_cw",
predictor_par = "b_hu_pushing_self_cw",
interaction_par = "b_hu_pushing_self_cw:barriers_self_cw",
exponentiate = TRUE,
vjust_val = -12,
) + coord_cartesian(ylim = c(1, 18))
p_odds_ratio# Export
ggsave(
filename = file.path("Output", "InteractPlot_log_odds.png"),
plot = p_log_odds,
width = 8,
height = 5,
dpi = 300,
bg = 'white'
)
ggsave(
filename = file.path("Output", "InteractPlot_odds_ratio.png"),
plot = p_odds_ratio,
width = 8,
height = 5,
dpi = 300,
bg = 'white'
)p3 <- conditional_effects(
pa_sub,
dpar = 'mu',
effects = 'pushing_self_cw:barriers_self_cw',
#re_formula = NULL,
plot = FALSE
)
p3[[1]]$estimate__ <- exp(p3[[1]]$estimate__)
p3[[1]]$lower__ <- exp(p3[[1]]$lower__)
p3[[1]]$upper__ <- exp(p3[[1]]$upper__)
plot(p3, ask = FALSE)# Expected physical activity
p4 <- conditional_effects(
pa_sub,
effects = 'pushing_self_cw:barriers_self_cw',
#re_formula = NULL,
plot = FALSE
)
plot(p4, ask = FALSE)Analyses were conducted using the R Statistical language (version 4.4.2; R Core Team, 2024) on Windows 11 x64 (build 26100)